Injector Housing to Head Port Match Issue

[KJL]

While addressing an issue regarding injection housing fuel injector seals, Jerry, from Jerry's LT5 Gaskets and Parts pointed out the housing I was describing was not for my 95 ZR-1 but for an earlier model engine. After pulling the intake plenum i noticed a port miss match between the injector housing and the head. Didn't think much of at at the time but given this new information, I thought I would attach a photo that represents the issue. Some ports are a bit better but this was one of the worse cases. Please note that the housing was ported by the previous owner who decided to use a non-stock housing and intake plenum for porting and powder coating. Unfortunately he no longer has the original parts. I guess my question is, is this common, if not, what can be done to fix it or at least improve it?