I've got a set of '84 ATC70 cases and a set of old (early '70s) CT cases sitting on the work bench right now, so I went out and did some checking, and I'm pretty sure that they are identical. My ATC cases are already machined for the left end of the kickstarter shaft and have the boss on the right case half that the return spring hooks on. If I was a betting man I'd say that it's easier for Honda to use the same cases for everything. They do have different numbers on the microfiche, but I don't see any difference, except that the ATC has the external cam chain adjuster screw and the CT doesn't. Just make sure you use the ATC cam chain adjuster parts and you should be good.
I've got assume that fatcaaat knows which kickstarter you need. Sorry, but I don't have the time to verify which one it takes right this minute.
Rysem steered you right on the shift drum stem. You can unscrew it and pop the seal out and replace it with a plug. (I think that 90801-035-000 is the number for XR/CRF 50/70s, which should work for you. Let us know how it turns out.
-kevin