We had the same problem, 2 years ago, Dan, when we installed my 409 in my 64. I tried to save some time, by installing the complete engine, and 4 speed, minus the carbs and distributor. It didn't matter which way, we angled the engine. The right exhaust manifold, would not clear the frame.
When we got the manifold, past the frame, it scraped the firewall, and got hung-up.
Very frustrating.:eek After, we took off the manifold, the engine dropped right in.
All of us, learned a few new cuss words that day. Good Luck, with your project. I hope all goes well.