Thanks to all of you for the great counsel and advice. I had my buddy from the VCCA who is very knowledgeable on stovebolt engines come over today and look things over. He agrees that the best way to proceed is to leave the transmission in place and set the engine in, mostly because of that strange universal joint mentioned earlier. Apparently he has tried it the other way on a '49 truck, and it did not go well.
I'll try the trick with the line-up punches and laying on my back while my helper adjusts from above with the engine leveler, which I have on order. I used a cut-off section of mainshaft as a clutch alignment tool, and it looks like everything is lined up OK.
Apparently the engine is not too tight after all. It takes about 45 ft-lbs of torque, applied at the harmonic balancer, to turn it over. I was basing my concern on inexperience with babbit-bearing engines. Looks like we are good to go! Hopefully I will be able to report in short order that I have it all together.