Using a 2x4 or something similar can help leverage moving the beast around.
You'll want to try and get the mounts as close as you can before installing them (too late now I think), that will save you some time being in uncomfortable positions.
Patience is required probably more than anything, it may take you hours. If you can get a helper to turn nuts on one side of the engine you can't reach that can save a lot of time.
The acceptable gap is usually the based on the diameter of the coupling, so if its a 4" coupling your acceptable gap is up to .004 inch. As mentioned, if you have a drive saver of flexible coupling they will have to be removed, you need to be checking the face of each. BTW, the coupling should be fitted to the shaft by a machine shop. I would do this even if I were using the same shaft & coupling just to be sure, its a $100 or less probably.
I did just what you are doing to my old engine, I replaced the mounts and did the alignment myself. I did okay but made one mistake...I used the shaft tube to get the approximate center for the shaft. It result in uneven wearing of the cutlass, slight but nonetheless. What I learned from the mechanic who did the majority of the install on our new engine, was to hold the shaft and turn it while feeling for resistance in the cutlass bearing, therefore you're aligning it with the cutlass not the shaft tube. I hope I worded that well enough for it to make sense.
My last piece of advice, if you have any doubt, have a mechanic check your work...it could save you easily many times the cost of repairs down the road! Just say'in
Good luck, its fun to DIY