Normally the rod shouldn't touch the crankcase but it's possible in yours that manufacturing tolerances have stacked up enough to allow a slight touch. If it were my engine I'd check the rod to find the high point where it's touching and carefully file/sand that area to give some clearance, maybe enough for about a .002" feeler guage to slip through. Chances are that if you leave it as it is then you won't have any problem other than maybe a blown plug if a bit of alloy rubs off and gets on the plug coil.

As for the crankshaft, with no prop fitted there's nothing to stop the crankshaft being pushed back inside the ball races other than whatever fit is used. There's a steel shim washer fitted between the front bearing and the prop driver and that shim sets up any axial play inside the bearings as well as putting prop nut tension only onto the front bearing's inner race. This movement doesn't happen in engines that use a split collet arrangement because even without a prop the collet still grips the crankshaft tight enough that hand pressure won't shift it.