The PCV is know as a "piggyback" as it rides between the ECM and the rest of the sensors, ignition system & injection system
SE Tuner (currently SEPST - or Screaming Eagle Pro Super Tuner) is an interface module that allows a PC to talk to the ECM, re-flash tunes into the ECM, it will hold a few tunes in it's memory - and also can be setup to log sensor inputs (good for drag racers to watch what their engines are doing on a run) to review and revise tunes. While they don't have it for the VRSC's, it also has a function called "smart tune" which will suggest tuning revisions based on what has been "logged".
PCV has a number of "base tunes" that can be written into the PCV module via computer and included software, and has the capability to add Wideband O2's, to create a "trim table" that will allow it to further modify the base tune in the module, based on the AFR data the O2 sensors are sending. Using this and a "close" base map in the module will (supposedly) "automatically" correct differences in the base map and actual running conditions of the motor. There are also a number of base maps to be found here on the forum, and around Al Gores interweb.
SEPST has a number of tunes included from Harley, pretty much for only HD OEM mods. The Factory ECM does not have the capability to read wide band O2 sensors, but the OEM "switching" type narrow band O2's and ECM are capable of adjusting within +/- .5 AFR (along with other variables such as knock sensor, Intake Air Temp sensor (IAT), Manifold Absolute Pressure Sensor (MAP), Head and Coolant Temp sensors.
BEST RESULTS are ALWAYS OBTAINED FROM A DYNO TUNE by a competent tuner. Any shop that tunes HD's will know how to tune with SERT or SEPST or the other HD OEM variants. YMMV when it comes to tuning other piggyback or ECM replacement solutions.
The more you mod, the more likely you aren't going to find a dead-on base tune, and will need to invest in dyno tuning ANYWAY.
If you're just doing pipes and aircleaner - pretty much ANY of the 3rd party piggybacks or ECM's will do the trick.
In my personal (albeit somewhat limited) experience (PCV, Thundermax, SEPST), I got the best, most STABLE RESULTS with the SEPST and a solid dyno tune.
V Rods, with their dual throated throttle bodies (as opposed to EVO & TC's) require both cylinders to be tuned individually (which of course takes 2X longer). A shop that does a lot of V Rod work, will have developed a library of tunes (other than the HD provided ones) that will get the job done much quicker.
Now here's where TRUST COMES IN...
EVERYONE will tell you their tuner is the shizzizle. Harry Potter doesn't work here - there's no "magic black box" that will automagically make any bike, with any mod, run PERFECT (or sometimes even not run like dogshit).
Plan where you want to END UP. If you're going the whole 9 yards (heads, TB, cams, etc.), do it ALL AT ONCE - so you only have to TUNE ONCE. As close as these systems manage the engine, pretty much ANY MOD is going to require a re-tune - or in the case of auto-tuning systems - a pretty spot-on base map as a starting point...
Before (heads, cam, 58mm TB, pipes, topless, K&N aircleaner, Thundermax autotune):
After: (heads, cam, 58mm TB, pipes, topless, K&N aircleaner, SEPST & 100 dyno pulls)
Deponent Further Sayeth Naught...
Rick
PS - While googling around for something else - found this interesting rundown on HD EFI and fueling systems:
http://www.nightrider.com/biketech/motorcycle_efi_upgrades.htm