2007 GSXR600 Electrical Issue Please, Need help!!!

I took my bike to a shop to adjust throttle body, install power commander (PCIII) & other work. I get my bike back & riding on freeway. I downshifted & gunned it. At the moment my bike started to flickered on/off, on/off (meaning losted power then regained power) really erractically about 4/5 times until finally regaining constant power with the "fi" light on. Everything is fine at this point. I get home, park it, turned off bike then about a minute later restarted bike & "fi" light was no longer on & bike ran fine. Flash forward 1 week later after bike just sitting. start bike, ran to gas station then bank (about 5 miles) to get ready for a ride. came back home, popped out clutch lever while bike still running, pulled clutch back in to start bike back up & bike would not start. didn't have enough power to crank over. after several attempts to find out cause of issue & 3 batteries later, i find out the shop i took it too installed my power commander on the top injectors (PCIII is supposed to be installed on the bottom injectors). The issue that i am dealing with now is the bike will start up fine once taken off my battery tender with a full charge. but, when i ride bike from point A to point B (my location) I turn bike off & turn bike back on and the starting is very sluggish & hard to start. It lost power somehow. I am wondering if the incorrect installation of PCIII may have caused my ECM to fry & could be causing this issue. Can anyone confirm this or give any feedback as to what may be causing issue or has anyone had this same thing happen to them. Please holla!!!

Note: my charging system is fine. replaced rectifier & stator with new ones. battery is good & charges 13.5-14.5v. I have no current draws no other aftermarket parts.  

First of all you should find your receipt from the shop that installed the PC3 and did the other work and get the work order from the shop that fixed the other shop's screw up and take them both to the messed up shop and get your money back. Then, I would go over all the wiring that's involved in installing the power commander and make sure it's all correct. The power comander is connected to your bottom injectors, battery, and the throttle position sensor. I'm assuming the problem is either a bad connection with the battery or the TPS wasn't installed properly causing the crazy power surges.

I installed my own on my 04 750 and my buddy's on his 09 600 and I know how much of a pain it was getting to his lower injectors and the TPS on both of our bikes. So double check the TPS connection on yours and be sure to apply a little dielectric grease to the connections while you're in there because I'd bet the chop shop probably didn't.  

But, the power commander is no longer on there as of right now. I took it off to try & isolate the problem. Everything is hooked up the way it should be. My problem right now is: battery is fully charged, start bike to warm up & it starts really buff, a lot of power, take off from home & ride for, lets say 20 miles & get to destination, turn bike completely off, then turn bike back on (regardless of how long it sat) then starting it up will be really sluggish. My thoughts on this is maybe i have a performance issue & not an electrical issue. Can anyone confirm this, give feedback or has experience these events?  

yeah that's a weird situation. Almost like a fuel pump starting to go bad. If it was any sort of messed up wiring or whatnot the bike wouldn't run properly right from the get go, but it sounds like once it heats up something goes out of whack.
tricky...  

Dave Sonsky,
The fuel pump seems to be fine. I could be wrong but, it seems as though I am losing electrical power as I am riding or losing it between the time I turn off the bike & turn it back on. However, it's regardless if it is a second later or 20 minutes later, etc. Maybe it has to do with something heating up then drawing power or not delivering enough power. If you were to eliminate the fuel pump out of the equation, could you think of anything else? How about this. I take my bike to Berts Mega Mall in Covina and they put a amp meter around the power cable coming from +terminal of battery to the starter relay. Here's where it gets tricky. The amp meter is polarity sensitive. The amp meter was facing up clipped on the cable & reading it from left side of bike (sitting on bike). The amp meter showed a -negative amp draw of like -3.### AS THE BIKE IS RUNNING. Did the tech have the amp meter hooked up right as far as polarity? or, Do i truly have an amp draw?  

By the way, love the articles.  

run the meter directly from the stator and test it.
keep in mind that just 'cause you replaced a part doesn't mean it's good.
20 minutes is just enough time for a bad reg/rectifier or stator to mess things up and drain a charged battery.
i replaced a reg/rec on a CBR only to find the new one was bad. it drove me nuts for months actually.
turns out it was the neg ground wire was loose where it connects to the motor, yet i thought that b/c it was having charging issues it was the stator or reg/rec—i changed both those parts, replacing one good reg/rec with a bad one!
once i tracked down the loose/frayed wire i had to backtrack and replace the reg/rec with the original.
then guess what—bike ran like a champ!
this is all after I took it to a reputable bike shop who told me the problem was b/c the carbs needed cleaning (they were totally fine of course).
frustrating my friend!