JDM swap issues

I recently had a JDM 2nd gen swapped into my st185 and was wondering what sort of issues there might be relating to the differences between JDM and US versions. I ask because the car has started overheating after highway trips and is knocking (94RON gas) at about 2300 RPM around town, after reaching operating temp. The car is currently in the shop that did the swap.
Now I'm no mechanic, but I was thinking one cause may be the EGR system. So I check out my parts bin to find the old EGR parts (like the valve) from the original engine and realized the old US manifold is on the car - because the manifold I have lying around has no EGR - just an undrilled bung on the manifold. Should I be using the JDM intake manifold? Even if this is not causing the overheating/knocking, are there any other issues with this swap? I know Japan uses higher rated gas, but would that cause overheating?
BTW: The car is currently stock aside from an IC fan and boost gauge.
Thanks

If you just swapped the motor you shouldn't have to worry about detonation since your on the stock US ecu. It sounds like you might have gotten a crappy motor.

Could just be plugs...
Maybe dirty inside...
How is your ignition timing?
Maybe no egr if it's a US ecu. I'm currently running a welded shut egr, but I think my engine is knocking (tiny bit, can't even hear it), 'cause I have kinda low power. Going to swap a new pipe in and see....

:?

UPDATE:
Called the repair shop and and they said "the oil is very watery," which I assume means coolant in the oil. I'm thinking HG. The swap is under a 6000 mi warranty, and it's only been 2000 mi. I'm just sick of not having the car - the new tranny, clutch and TWM shifter are soooo nice.