Nice one Declan! Look forward to seeing it all complete.
As for the cruise, I had a similar issue when I did my engine swap. It will fit and work normally with the standard intercooler, but with most aftermarket ones it won't as you've found out. I ended up pulling all the cruise control parts out of the engine bay as I barely used it anyway.
Just be wary if the ECU is reprogrammed, might be tuned to suit high octane Jap fuel