Of the half dozen 727s I've done...I've never checked that line-up. Personally, don't think it's needed. All this stuff is cut on a fixture, to keep things in line. But, it's your dance!
When I do get extreme, I use a pane of glass, since their perfectly flat. If, and when, I want to check things, I'll look at the flexplate, since it's critical to that spinning mass, and the run-out of the shaft.
All three, or four of the mounting faces on the plate need to be flat. Placing the flexplate on the glass will show if the mount faces are in line. Checking if it's square...flip it over on the glass, and measure each, to the glass.
Anyway, never had a problem, as long as that flexplate is good.
Another subject - anyone use MAKCO Transmission parts? They seem to have a pretty complete inventory.
Bet their prices are higher. Too easy to get good overhaul kits, from a supply house.
Is the Transgo TF-1 valve body mod a good idea?
I'd call that...up to you.
In your handbook, there's plenty of proven mods, that can be done.
Sounds like your's will still have decent parts in it (maybe), but, look everything over. If any doubt...replace it! Look for wear, parts burnt, and so on. On the pinion thing, it only takes one bad gear, to make the cage bad...so, carefully check 'em. That handbook will tell you most of what you want to know.