I have the opportunity to buy a JDM Integra Type R transmission for my USDM GS-R. I know the JDM ITR engines have different flywheel gearing, so will a JDM ITR transmission bolt right up to a USDM GS-R engine or do I have to get some new stuff for it?

Yep - should bolt right up with no difficulties. Make sure you get the LSD with it! That's where the gains are - although the shorter ratios are nice. Will seriously improve track times with LSD+gearing.