Did you use a distributor to locate the intake manifold? If not, it can be off enough to bind the distributor up, or just stop it from dropping in. That doesn't explain why it won't drop into the old engine though, but it's still something to check. Have you measured and eye-balled the gear to make sure it's the same diameter, tooth size etc? One last thing to check would be the hole size in the intake. I forget what intake you used, but aftermarket parts are always susceptible to machining errors.