Perhaps things are OK.

Not a build day, but as mentioned in my last post, I was worried I'd damaged the backpate of the engine. Well, I've bolted the gearbox back on on the bench (minus a clutch) and everything seems fine. If anything was bent, it was bent back into place.
So, I've ordered a new clutch plate and this time I will assemble everything out of the car, then look at ways of installing the engine with the gearbox already attached.