02 gsxr 1000 misfire/loss of power

to make it short, a guy pulled out in front of me, i ended up dumping the bike, only replaced frame sliders and the engine cover left side with the stator attached..

her comes the problem, when i transfered the stator to the new cover i put the mag lead bracket in upside down test drove felt it misfire, took it back apart and found that out, I did bend it a bit too the first time but bent it back to basically normal (i'm not a mechanic) so now i put the bracket on right and it still is doggy at the start of every gear but at 4k rpm picks up and runs sort of normal.

I have GSX-R 1000 '02 9500 miles, full trs header and pipe w/ power commander.  

my questions what is causing the loss of power could? I hadn't rode the bike for a couple weeks because i broke my thumb and a buddy rode it to my place to park it so not sure if it ran fine before i replaced the cover or not.

I noticed the time had been recent like the battery got disconnected, could the power commander just need to be re/mapped?

let me know what you think.  

so i've been reading and one guy had a similar problem and it was the STV actuator?? anyone know if a power commander needs to be remapped if the battery dies?