Unless someone here has researched it, you might want to look at Maliburacing.com in the forums for the answer to the transmission options...I swear someone there said they had a 4-speed wagon, but don't hold me to that statement.
I know you could find them with TH-200's, TH-200C's, TH-350's, and some 4-speeds (Saginaw) in passenger cars for sure.......
My '79 coupe, 267 engine, came with a TH-350.
Sorry I can't help more.
On the fuel cell issue, as long as the cell is enclosed in with the proper materials, and isolated from the driver compartment (minimum .032" aluminum / .024" steel) you could stuff it in the spare tire well okay.
Not having a wagon, I'm guessing that the spare tire well is under the rear floor, with the wheel flat?