piheads

Hi I have a 1997 GT and I decided to do a PI intake swap and the gaskets needed no modding and the intake sat perfect but I noticed that the non Pi intake I took off, the gaskets didn't line up correctly and we're actually partially in the intake holes. Is this a clear representation that I have...

I have a 98 GT mustang with a pi head swap. I'm trying to figure out which tuner I should use since there is a large compression difference from the stock heads. Any help is appreciated in advance.