Oh right, I forgot you have the case halves together. I've never put in the primary shaft assembly with the cases together but I'll reference the more knowledgeable Dave500 in his second reply that they can go back in but with just a bit of wrangling. It would have been easier to do it with the cases apart but shouldn't be a problem that you didn't.
Just so I can visualize this, you're doing everything through the oil pan, right? I see what you're saying about trying to put the clutch in first and there not being enough room to get the gear on. I'd try again first assembling the clutch and gear and trying to put it in the chain while rotating the crank a little. In my imagination, and honestly relatively little knowledge about these bikes compared to the old timers, that would be your best bet. I don't have any tricks up my sleeve for this, sorry. Just be sure the primary chain is fully seated on the crank sprocket teeth.
Maybe post a couple pictures just to make sure you have parts installed correctly?
---
1978 Honda CB550K