FMS / Fuel Controller units 

Many riders have gone with an aftermarket fuel management system wanting to eliminate the lean condition (high air/fuel ratio), primarily so it seems to enjoy a smoother running engine with better throttle response while also reducing the engine's operating temperature, most evident when riding in stop & go situations and at slower speeds.  The bike's ECU actually does reasonably well responding to a number of ongoing changes that can and will occur, even to include a new exhaust system, yet when those changes include adding both a new exhaust and air intake, the engine will then more noticeably benefit from having the FMS.   

If you make a change like this, even if you don't, it remains to be a good idea to occasionally check (and clean) your plugs to learn if they give the appearance of you bike running a little too lean (or rich with the FMS).  Due to the EPA's emission standards, the stock fuel management setup is on the lean side, many think way too lean.  Here's a link that shows you what the plugs look like under many conditions.
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IMPORTANT SIDE NOTE - NOT to be overlooked:
This comes as a highly appropriate friendly reminder from MaiKai:

If you install any FMS/Fuel Controller, once completed, rather than starting the bike and enjoying a nice ride, it is often much better if you first disconnect one of the battery terminals for a few minutes and then reconnect it (good time to add some 'dielectric grease').  This allows the ECU--electronic control unit-- to better recognize the change(s) made and recalibrates itself accordingly. 

This same effective procedure applies to when a rider adds Jack's O2 Sensor Mod, or anything else that might alter even slighty the engine's air/fuel ratio.

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EJK - Electronic Jet Kit <-- click here  (also see info listed under "Techlusion" fuel controllers located below)
A premier fuel controler manufactured, sold and warrantied by EJK, a company located in Montana and owned by Mark Dobeck. Mark and his brother, Mike, created Techlusion. Mike's company, Total Fuel Systems in NV, manufactures the Cobra fuel controllers. Mark's company, EJK, manufactures excellent fuel controllers that work in a way that is slightly similar to the Cobra Fi2000r controllers, but with the added flexibility (no dyno required) of allowing the rider to modify when each of the settings take effect within the engine's power band. These EJK controllers include a 30-day money-back guarantee, along with a full 2 year guarantee, whereby EJK will itself repair or replace any unit that needs servicing.
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Cobra FI2000

The Cobra unit is commonly used today and allows one to adjust 3 different pots (see the description below as to what each pot controls). The factory setting is 1-3-1, and some will find that to work well, "based upon which mods are on their bikes.  

The standard type of Cobra Fi2000 models:

• Open loop - In this case the unit is installed inline but the O2 sensor is disconnected
• If you have emissions tests in your state, it could fail.

• Here's a YouTube video of the open loop being installed on a V-Star 1300.  It's pretty simple!

• Closed loop - In this case the unit is installed inline without any other changes required
• The majority (but not all) riders using one of these two Cobra Fi2000's are using this model
   

(Added, thanks to MaiKai)  Discussing for a moment only these two Cobra CLOSED loop and OPEN loop controllers, as mentioned above, the CLOSED loop is what the big majority of 1300 owners have with features that benefit the bike very well.  The known advantages of using the CLOSED loop controller are three-fold: 1. One's bike will continue to benefit from utilizing the O2 Sensor; 2. Even as a CLOSE loop fuel controller you can adjust the 1st (green) pot if and as needed, done so mostly to reduce the amount of popping coming from the exhaust which is heard during deceleration.  Rarely when using an aftermarket exhaust will the popping/gurgling be completely eliminated, and that is perfectly fine and to be expected;  3. In an extreme situation, one can disconnect the O2 Sensor (generally should NOT be necessary) and use the unit as an OPEN loop controller, whereas the OPEN loop controller can be used only in an OPEN loop configuration.  In that rare case when the OPEN loop is desired in order to increase even more the fuel flow from the point of 'start-up' to low to mid RPM riding, it would then also be a must for anyone who had previously installed Jack's O2 Mod to remove it because it cannot be used without also using the O2 Sensor.   Overall, the advantages weigh "heavily" in favor of using the CLOSED loop fuel controller the big majority of the time. 

Description of the pots:

GREEN LED POT (left pot) – With the Closed Loop function of this module you do not need to adjust this setting, leave it at 1.0. Without a closed loop system this adjustment would affect idle and cruise fuel. If you had cruising issues, this is where you would try a different setting. Generally, surging and uneven running while cruising is a lean fuel condition, so adding a small increase in fuel by turning this adjustment clockwise with a small flat blade screwdriver a 1/2 of a position would help. The bike would need to be Test-driven to feel an improvement and only the setting would need to be increased until the surge went away. Also, backfiring or popping on trailing throttle is generally a lean symptom (or an exhaust gasket leak). The same small increases as above would be tried just until the backfiring would disappear. 

YELLOW LED POT (middle pot) - this adjustment affects acceleration and power fuel. If you have a hesitation or bogging on acceleration, this is where you would try a different setting. Aftermarket air cleaner assemblies generally lean out fuel mixtures, so try small clockwise increases until a smooth acceleration returns. Starting with the base setting, test ride the motorcycle in 4th or 5th gear and perform moderately fast roll-on throttle from a repeating standard R.P.M. or speed. Increase the pot one position at a time and stop as soon as you don’t feel any improvement.

RED LED POT (right pot) - the right hand or red pot is for the fuel setting required when the engine is maximizing its R.P.M. and power delivery. This pot is similar to the main jet in a carburetor. It will take a combination of a minimum R.P.M. and a predetermined amount of engine load to initiate this fuel. The straightaway on a racetrack or an inertia dyno are the best places to set this pot. Full exhaust systems of high quality construction increase flow characteristics and will increase fuel demands over our base settings. Also, air filters specifically designed for higher than stock airflow can create need for higher fuel setting. Try an additional one-position pot setting at a time.

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Cobra - PowerPro Tuner ......    see it HERE

This is the newest and most innovative "mack-daddy" of the Cobra fuel controllers.  Its cost is about double of Cobra's standard fuel controllers, but to many who have been able to afford it, it is excellent.  This fuel management system uses the latest smart chip technology to continually read the bike's EFI's fuel delivery at up to 80 times per second every time the throttle is opened, this to optimize the air/fuel mixture at all throttle settings.  With its Continuously Variable Tuning (CVT) (patent pending) technology, the PowrPro has revolutionized motorcycle fuel-injection tuning.

With PowrPro you can say good-bye to old-school EFI "mapping mania" and O2 sensor hassles forever.  When your bike accelerates, PowrPro reads the engine's performance up to 80 times per second to optimize fuel delivery at all throttle openings under acceleration, under every kind of load and under all existing environmental conditions to deliver maximum acceleration and efficiency. 

 And no matter which components you change in the future, whether it's a new exhaust system, a free-flowing air filter setup, or more, PowrPro will continually analyze and properly tune your engine. 

NOTE:    the vast majority of riders using this exceptional CVT fuel controller have given it 2 thumbs up, acknowledging its added overall efficiency and benefits provided.  The newer CVT units, since around the beginning of 2013, have been made with a single dial which does allow the rider to fine-tune their low-mid RPM fuel settings if they found that their bike would benefit from increasing the fuel flow during those times. 

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Power Commander

Here are directions for installing the Power Commander.

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TECHLUSION /Dobeck Performance....(aka "EJK" - see EJK controller information above)  (information here is provided thanks to our friend, Steve Melb, from "The Land of Oz")

http://www.techlusion.com/dobeckcontrollers.asp 

There have been considerable developments seen from Techlusion during recent times with the very highly regarded pushbutton Gen 3 & 3.5 versions.  
http://electronicjetkit.com/Cruiser/default.asp  <--- Click here to find information on the Gen 3 FMS that Mark Dobeck recommends for the V Star 1300, indicated by part #9120292.

Those who have been using these newer FMS controllers are almost unanimous about the very positive results experienced.  Additionally, this controller supposedly works equally as well for the 1300 regardless of the country where the bike was purchased and is being used.

It may be very well worth the time to contact the company to gather whatever information and/or answers you seek.  You many be very glad you did.
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The older Gen 2 TFI Techlusion is similar to the standard model Cobras, however there are two distinct differences:

1) The Techlusion has only one model.  It is capable of being used with or without the oxygen sensor connected.

2) The Techlusion has a 4th adjustment.  It sets the RPM at which the 3rd pot takes effect.

     Green LED pot (1st)

Air fuel mixture screw adjustment. With TFI installed and the bike fully warmed up,

screwdriver in hand, locate the green LED and the pot right below it. Using the throttle raise the RPM to a

high idle or about 2000-RPM. Once there, slowly turn the green pot clockwise from the 1:00 position (off)

until you achieve the highest RPM and smoothest running sound (like a mixture screw on a carburetor).

You should find the best setting between 2:30 and 4:00 o’clock. If you turn the green pot clockwise and the

engine does not accept any more fuel (RPM drops when adding fuel) you may have one or more of these 

problems (See troubleshooting Motorcycle).

       Yellow LED pot (2nd) 

ACCELERATION FUEL ADJUSTMENT (bottom to mid range fuel)
Anytime the yellow LED is on, this pot is adding fuel. In neutral raise the RPM slowly up through the

mid range and see no yellow LED.  However, opening the throttle quickly from idle you “should” see the

yellow LED come on.  Fine tuning: Start with the suggested setting and then add ½ clock position at a time

until the bike says too much (hesitation) then back off 1 clock position, if worse go opposite direction.  If no

yellow LED there is not enough load to turn it on. At that point the street or dyno will be able to show the

difference.  The yellow pot adds its fuel below 70% of maximum RPM.

     Red LED pot (3rd)

MAIN JET FUEL ADJUSTMENT (top end fuel)

It adds about 2.5 points of main jet fuel with every clock position. For example, one clock position is the same

as 150 to 152.5 main jets.  Fine tuning: Start with the suggested setting and then add ½ clock position at a

time until the bike says too much (hesitation) then back off 1 clock position, if worse go opposite direction.

The red pot adds its fuel above 70% of maximum RPM.

     "RPM" pot (4th)

All V-twins: SETS THE RPM THAT THE RED POT FUEL (main jet fuel) TURNS ON.

One clock position is roughly 1000 RPM.  This pot should be set to about 70% of redline. (For example: the

Yamaha VStar 1300 redlines at 6300 RPM and 4400 is roughly 70% of redline, which would be 4:00 o’clock).

On “some” dual plug systems (Kawasaki, Suzuki) you will need to double the RPM clock position to have the

same results. Verify setting by raising the RPM in neutral, look for green and yellow LED to shut off and

the red LED to turn on at the chosen RPM or refer to suggested settings if you have no tachometer.

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