Pc3 ?

[VA-hawk]

I picked up a 99 for dirt cheap for a 1397 build. It has a stock motor pc3 rs3 exhaust and was running good. I did a small air box mod and now bike surges downloaded a diff map and still surged so I unplugged the pc3 and surging went away. Could the pc3 have went bad at the same time as the air box mod what's the likely hood of that. Or could it be the fuel pump????