The flywheel position does not matter unless you use the marks on it (through the peep-hole) for timing. (Relevant to earlier 3A's)
I wouldn't mess with the head if it isn't leaking.
If I didn't know who rebuilt the motor, I would pull the pan and valve cover to check everything; You might as well adjust your valves while it's out too. Check for any extra play on the rod bearings and your end play on the crank.
If your engine does not have the timing marks on the timing cover I would suggest doing something like this
http://www.thecj2apage.com/forums/diy-timing-pointer_topic12750.html as it makes timing the motor a breeze!