Been awhile since I updated my situation, so here goes:
To be 100% certain the gasket I ordered wasn't an issue too, I bought a copper gasket from NewComer Racing, which fitted the block like a glove.
Had the machine shop use the copper gasket as a template and they re-drilled the holes on the headers.
Perfect!
Onto the next issue, the stock inlet manifold didn't fit.
I ended up taking a angle grinder to the inlet manifold in a couple of places...
I was going to continue fitting up the SC, but I needed the TJ while the other car was out of action, so ended up putting everything back together for the time bring.
Don't know why, but went with a aFe 3" cat back.
The whole system has had about a month to settle and these are the results:
Cold Start:
Snap, crackle & pop:
Warm start & drive:
Slow(ish) drive: