That's interesting thanks for the info littlewhiteute, you seem to have all the answers! And steptoe of course

I understand now about the thread sizes, had a bit of a "DUH!" moment

Also makes sense about the big ends being caught up because they are loose, good news as well.
I'll have to take a pic of the crankcases alignment, it may not be much but it looks more than before I took it apart. The "step" of the misaligned parts is only on the top and back of the engine, down where the sump is the two parts are flush. Maybe it's fine and I'm just making a fuss about nothing, it's happened before
For the stripped thread since it's only 5 ft/lbs at the most (practically nothing) could I get away with making a new thread out of epoxy?

Completely dodgy I know and I wouldn't do it normally but dunno when or where I can find a helicoil, and if everything else is ok (alignment) it's alot of bother to fix one thread that doesn't do much.
steptoe if this was a customer car I would ask my boss why he's getting a first year apprentice to build an engine...if I still had a job by this stage
*edit* Never mind, I must have been imagining it, the cases are a bit off but all the seams are completely flush where it counts (oil pump housing, where the oil seals go etc)