My Z1A engine went in in one piece, so yours will come out. The only significant thing not fitted was the oil filter. I don't know for sure but I don't see why you wont be able to get at what you need to by just turning it upside down and splitting the cases, without disturbing the top end at all. If not someone will be along soon to call me an idiot.

Totally different bike, but when I rebuilt my CL450 barn find, I had exactly the same sort of sh*tf*ckery with the kickstart. That was as simple as the fact that I should have turned the shaft to preload it before fitting the kickstart spring into the hole for it in the shaft. Nothing was broken or bent, it just needed doing right, and its now perfect. The upside with that bike was that the engine didn't have to come out again, I just had to take the primary drive off to get at it.