KPRO troubles???

I haven't driven my EP for almost a year. it has been sitting for a while and rats got into the password JDM injector wires and chewed up several of them I replaced. so I replaced them and the spark plugs. it still has misfires in 1 and 2 cylinders. I swapped the coils to the other 2 cylinders and it still remains to misfire in 1 and 2. so I wanted to check my calibration since my battery had died over the time sitting. but KPRO wont communicate since its old. so I updated the software and it still doesn't communicate. what else do I need to do? I saw that there is a V3 KPRO. do I need to send in my ECU to be updated?

to answer your question about upgrading:

"Upgrades

Any current K-Pro owner may upgrade their old working K-Pro for $250 using this form."

quoted directly from http://www.hondata.com/kpro_v3.html