While it is apart, change the water pump and the timing chain. Recovered to use authentic Ford parts. Put in Ford yellow antifreeze and distilled water. Lots of info on the internet about this
We put a truck motor in a 706 that had a bad motor. The crankshaft in the truck engine sits either higher or lower in the block. I don’t remember exactly. We carefully lined up everything and drilled some new holes. That was over 30 years ago and tractor is still being used.
Have to have hydraulic pressure for TA to do what you want. Take the inspection plate off on right side of TA housing where flywheel is located. Use a bar with a flat end on it and pry on the flywheel ring gear. You have good leverage there.
I saw your post on the sheet metal problems. I sold several salvage 50 series to a local guy so you might give him a call. His name is Jeff Ewoldt and he works in the service dept at Ne. Pererbilt here in Grand Island, 308-382-1044