I know the answer because I put a d16a1 in my 89 crx si.
The motor will fit, but this is what i had to do:
1. tranny and block only match 4 out of 5 bolts, but still works.
2. CYL sensor needs to be rewired, and the distributor plug needs to be modified to fit the A1 distributor also.
3. 2 vacuum lines need to be sealed.
4. I only had 3 motor mounts, no driver's side mount.
5. no knock sensor on A1 block, so no need to hook that up.

That's all, and the engine fits and runs great, BUT here's what happened with the motor running:

1. raced a del sol non-vtec and I lost.
2. after that, I turboed it and 7PSIs blew valve seals.
3. rebuilt head after that.
4. after 395 miles with this motor, It threw a rod.

In conclution, the motor will work, but it has NO potential as a high HP motor, no potential, did I mention no potential?