The easiest swap would be a 89-90 Integra motor with tranny. Keep it simple. Their is a cable clutch in the car, why go through the headache to convert it? The swap uses the exsisting mounts, with one modification as long as you get the rear mount bracket from the integra. If your CRX is and SI then even better, less wiring to deal with. The swap is nice with good power and clean installation. I have done it, but took a carb. automatic CRX and swapped a ZC with Fuel injection 5-Speed. Took a month, but the customer was happy and the car ran solid. If you have any questions I can help as I take notes on all the swaps I do.

On a side note, one other advantage to going with the older 89-90 is that you can usually find this year CRX or Integra in a pick a part yard. It can save big $$$ to pull the part you need yourself.