I Think I Fried The Ecu

bit of help , a wile ago i fitted a second hand power comander 3 to my 2005 speed triple as i thought it would smooth it out a bit as it has a K & N filter and a single race can fitted with a O2 eliminator.
well long story short the PC3 did not work at all so it was returned , and i went to put it back to the way it was , that was when i made a massive cock up by mixing up the fuel pump lead and the o2 sender leads .
the bike did not start and then i noticed what i had done and put it back and it ran but not that well .
the bike will start and tick over and run just fine but runs just on two cylinders on the way home i have tried to re set it many times and just when you think its ok it plays up , can i just replace the ecu ?
i have now put the om pipes back and the o2 censor hoping it would fix it it did not

 

no the fuel pump is fine i have done the start with no throttle and run untill the fan starts but the the yellow warning light says on , the bike runs ok on the way to work but when i go to ride home later it feels like its missing and you have to rev the tits off it just to get home keeping the revs at 4000rpm then the next day its ok ?? i have found a ECU so it may be a swap over

 

Reloaded the map , i have no idea how to do that

 

new plugs

 

Ok thanks I will have a look. I did do it on my buell a whle ago but then I had a cable and was sent the program