Finished up the reassembly today. Took extra pains to seal all gaskets/bolts. Applied a bead of sealant on all surfaces, installed dry bolts and lightly snugged parts to squeeze and spread sealant but not tighten fully. Then pulled bolts out one by one and coated them with gray RTV and reinstalled and then torqued tight. I sealed the vent holes in the lid gasket with RTV to keep the top of the gasket dry. Hopefully no leaks this time.
Below is a good set of instructions that I was given a link to. It's a little tedious to use because of all the separate photo links and some of the links to photos connect to incorrect photos. But it has some excellent illustrations of the main cluster assemblies and other sub-assemblies that are hard to find elsewhere. I printed out the main narrative and 3 or 4 of the sub-assembly pictures for good detail.
ClassicTiger: Ford Toploader Transmission Manual
Noticed one issue with my throw out bearing that I need to look into before reinstalling but I think I'll post it in the Transmission forum.