Clutch release arm and clutch plate was the wrong way.

[Toms306]

My dad told me a good trick for when I spit the box again. He said to get a couple of long M10 threaded bars, screw them in to the top bolt holes and then slide the box over enough to undo the cover plate. Thought that would be pretty good to keep very thing in alignment, just hope it's as easy as it sounds. I might even get away having to pull the N/S drive shaft out this way.

That sounds like a good idea!!

As for checks, I wouldn't have been starting it without any shafts/oil tbh so you can't really have done anything extra.