You mean on the master cylinder? That's a pig I'll admit though the clutch is worse on the Jem, as it has a centre console.
Fiddly too, but I use a slightly shorter bolt than the others so I can change the clutch plate in situ if necessary.
I now have the type with captive nuts. Brilliant solution! I drop the subframe if I want the engine out.
I use LCBs. All clamps easily accessible underneath. The early Minis used to break the flange on the down pipe because the engine rocked back and forth too much but you could get a flexible pipe to cure that one.
Manifold nuts are easy enough to get at. I just slacken them off enough to lift the manifold and carbs out together, complete with cables.
I've never done that to myself. You didn't mention getting the steering rack U-bolts in with the subframe in. The trick is to squeeze them up in the vice first so they go in easily.
The secret is to take them to bits often enough that they don't get completely rusted up. You also acquire the best spanners for awkwardly placed nuts and bolts.