There was a PILE of information on the old site but it was spread out and some of it (of course) was contradictory. This site is too new to have that much info. and unfortunately a lot of the old info. was new at the time anyway and isn't likely to be repeated. Put another way, all of us were going through the learning curve with C-14's and that phase is over; some of the great contributors / discoverers are not even 'here' anymore and have not been around for quite some time.
I can give you a brief overview for whatever that is worth....
There are basically two different aspects of tuning / power increase on the C-14; one is altering the air / fuel mix to have the bike run better and / or have more power (we are not restricted as Kawasaki is by the EPA), and altering how far and how early the secondary butterflies ('the 'flies ') open. Unfortunately these two things get mixed together because when the 'flies are removed the air / fuel mixture is usually changed by some other device. Because both things happen together and the fuel mix compliments the 'flies removal, it appears like they are related but that is not actually the case.
First the mixture: the air/ fuel mixture is set to meet emissions standards and may not be, and is usually not ideal for performance or running characteristics. Basically and simply put, the mixture is controlled by how long the fuel injectors are held open (open twice as long means twice as much fuel delivered per engine cycle and so forth), and the injector duration is controlled by a "map" or look-up table in the ECU on the bike. So the ECU gathers the data that pertains to mixture including throttle opening, engine RPM and looks for the 'cell' where those two things cross and use the number in that cell. That number is then modified by ambient temp., engine temp., barometric pressure and similar inputs (important but secondary to throttle opening and engine RPM) and uses them to modify the number that was in the cell and then you have a fuel injector 'on' time (which directly controls how much fuel is injected of course). There are two basic ways to alter the factory map: the first way is by using something like a Power Commander or similar which will contain its own map and lean or enrich the mixture by adding to or subtracting from the ECU's 'on' time. Example: the ECU chooses 45 milliseconds of 'on' time but the Power Commander uses its own map to determine that it will increase that on time by 10%. The Power Commander simply interrupts the signal to the injectors, adjusts the pulse duration ('on' time) and then sends that time to the injector.
The second way to alter a factory map is to reload ('flash') the original map in the ECU with another, custom written one. Basically the same effect as the Power Commander but it does not require external hardware.
The secondary 'flies in a C-14 are controlled by the ECU and will override the manual throttle plates (the ones you have control over via the throttle). They are only used at low and mid RPM ranges but significantly reduce engine torque (and therefore power) at those speeds. The ECU gradually opens the secondary throttle plates as the engine RPM comes up allowing a bigger and bigger percentage of available engine power to be used until they are fully open and no longer restricting the engine.
The biggest single performance difference available on a C-14, at least at low and medium RPM (below 7K RPM) is to remove those secondary throttle plates so they are effectively 'open' all the time. That way when you dial in 1/4 throttle, there are no other throttle plates ('flies) in the way which may only be open 1/16 throttle. Recently several companies have been offering a re-flash service for the ECU, and one of the things that can be altered is how far and how fast (at what RPM) the secondaries are open. Fully opening them all the time should also be an option on a re-flash. The re-flash can (and should) also re-map the mixture control map to compensate for all that additional air going into the engine when the secondaries would normally be closed far more than the main throttle plates.
If the 'flies are removed, then the air / fuel mixture is usually compensated either by using a Power Commander (or similar item from another company) or by re-flashing the ECU on the bike.
In addition to all of that there is the ATRE, which changes both the 'flies opening as well as the mixture by fooling the engine into thinking it is in a different gear than it really is. The 'flies open sooner in sixth gear so that is usually the gear chosen to get the most power out of a C-14. According to those who have used both 'flies removal as well as adding an ATRE, the ATRE is about 1/2 as effective as removing the 'flies. You could do both together but there is little to gain with an ATRE once the 'flies are physically removed anyway. By the way, the name of that device, Advanced Timing Retard Eliminator really does not change the timing beyond using the timing map for the gear chosen. Confusing, huh?
There are your options:
1) Add a P.C. and re-map the mixture. The bike may run better, get better mileage and there may be a slight increase in overall power but nothing drastic. About $300 and maps are readily available, especially if you buy the P.C. from FuelMoto as you can have all of their maps at no cost. You can also tinker with the mixture yourself with a laptop if you want to. Removing the P.C. will bring the bike back to stock. No physical mods. needed on the bike itself (the P.C. wires into a harness on the bike).
2) Add a ATRE. About $150 or so. More power in lower gears but the gear indicator will read incorrectly. Some ATREs come with a digital gear position indicator to use in place of the factory one so the correct gear is indicated. No mods. to the bike itself and simply removing the ATRE brings the bike back to stock.
3) Pull the 'flies and add a P.C. About $300 if you remove the 'flies yourself. Large increase in low to mid- range power. Possible increase in mileage although using the increase in available power will eat all of that and more possibly. The bike may run better due to the P.C. if the correct map is used. This one is tougher to undo because the 'flies have to be reinstalled and the P.C. removed. The 'flies need to be centered in the venturi of the throttle bodies. Also, if you break a secondary throttle plate screw when the 'flies are removed they can no longer be reinstalled (the mod. is no longer reversible).
4) Pull the 'flies and do nothing else. No cost. Some have reported good results doing this but I would be wary of the engine running lean. I don't have any data to support that though so I really do not know one way or the other. If you wanted to do that I would suggest having the bike tuned on a dynamometer to make sure the mixture was acceptable. Again, the 'flies have to be reinstalled to reverse this mod.
5) Re-flash the ECU. Cost seems to be around $400 or so. You should be able to get about any condition you want out of this mod. if the re-flash contains good data. In other words, if the 'flies opening routines are altered properly and the mixture maps are also altered properly. Undoing this mod. requires the ECU be re-flashed again with the stock data. It should be easy enough to do but will cost an additional $400 or whatever the first re-flash cost. Of course the bike will be down as it will not have an ECU while yours is being sent off and re-flashed.
This whole thing gets more complex on 2010 and later bikes with traction control because T.C. uses the secondary 'flies to control the engine's output should the rear wheel slip. There is not much info. on what happens to one of these bikes if the secondaries are removed and traction control is activated; the ECU still has control over the power output through the fuel mixture (it withholds fuel when the rear wheel slips) and retards the timing but because the ECU would also be trying to close the throttle but could not, the response speed of the traction control could be affected.
Well, I guess that wasn't all that brief. Not sure if I cleared this matter a bit for you or made it more complicated but like Big Al said- 'Make everything is simple as possible.... but no simpler'.
Brian
I usually understand most tech stuff better than the average person, but it seems to me that the average person on this forum is above average in the
tech area of intelligence. I am sort of understanding some of it, but with PowerCommanders, TREs, Autotune and then reflashing it gets confusing.
I've been trying to determine what is best for me to improve performance of my '10 connie, but I would like to fully understand what each of the options
is actually doing. I do not want to remove my secondaries, and I do not want to remove the spud launcher (I like ugly quiet better than less quiet). I'm leaning
towards a reflash or GoPro ATRE but I'm not sure what all my options are with the reflash. I could put what I think I understand on here and see if it's correct,
but then why wave my ignorance in your face? Is there a primer or a lengthy post that would sort of tie all these options together? I've been looking but I
haven't found one yet. Fred H.'s GoPro ATRE review was very understandable and I like the idea of Mode 4 that has no effect in first qear for slow speed control,
however I'm not so thrilled with the gear indicator stuff. 
So having said all that, I'll repeat....
Is there a primer or a lengthy post that would sort of tie all these options together to help me understand what each does?
