You can DIY on the harnesses and such, or there are several retailers that can help. For more $$, of course. I think the guys at
Rywire : can get you a wiring harness, but it does come at a cost.
The HF transmission (be sure it's an HF one, the 88-91 CRX/Civic transmissions are tough to tell apart from the outside!) and the CRX chassis are built to go together. The trans should bolt up to any D-series engine as far as I know. I'm not sure if the mounts on the Y5 are the same as the ones on the A6/etc. If so, then you're golden.
The drive axles in the HF, and the hubs and brakes, are different from the other CRXes. They're lighter-duty and lighter-weight. I
think the regular axles will plug into the HF trans, but I am not certain. If they do, then use whatever axles go with the chassis (and therefore hubs and brakes) of the car you get.
The guys at
CRX Community Forum • Index page have a lot of knowledge of these cars. You could do worse than looking around there for a while.
-soD