You'll want the engine set back as far as possible because the Front Engine Accessory Drive (FEAD) and your radiator setup will be snug. This is where your searching, reading, and planning will pay off.
Concerning the removal of the "hot-rivets".
You might consider removing the ones for the tranny crossmember to locate the tranny mount where it needs to be. There are other options, but rivet removal to relocate the tranny crossmember is viable.
The ones for the radius arm crossmember can be removed, and replaced with bolts, so that the radius arm crossmember can be removed. This is particularly handy if you install a large automatic tranny (like an AOD). An AOD will not remove very well between the small tunnel and the crossmember. You can force it, but its a PITA. Things forced tend to get broken. Then, you get to force it back in! Which leaves you with the only other option of pulling the engine and tranny together out of the "big hole"! Note: If you decide to use an AOD, modify the crossmember for removal. Ford uses 4 "hot-rivets" (2 on each side) going through the sides of the frame, AND 4 threaded fasteners (2 on each side) going through the top of the frame. "Hot-riveted" on the sides and bolted on the top! DUH!? Must have been designed by 2 separate engineers in different offices with no phones!
The only other "hot-rivet" to consider... If you do a body lift, you may need to relocate the one that secures the parking brake cable bracket to the frame. I think was "hot-riveted", too.
Another Note: Drilling, Grinding, Beating. Requires the proper tools. A 4" electric grinder is good - If you have it - air is good. (A Cold Chisel jus' ain't gonna' hack it!) They are hard and tight by design. When replacing "hot-rivets", always use (at least) Grade 8 bolts. And I recommend Nylock nuts. This is a task thats much easier done (planned) with nothing in the "big hole", engine and tranny removed. Be prepared to spend more than an hour, but its time well spent.
"Hot-Rivets" is subject matter for a topic in the Technical Library > Custom Fabrication. I'd be willing to write it up, if only a moderator would PM me and tell me how to make it happen.