Breather installed on the engine.. You can install it after the frame is on but it's a real pain in the arse.
Also Dont forget the straps for the battery that hook under the plate, every time I put a frame back on I forget..... 5 from 5 times now.
And I find it easier to put the tacho cable on the timing cover, again, just a bit of a pain in the arse to tighten up properly when the frame is on
Try and adjust your clutch arm to be in the right place as well, again access is limited once the frame is on.