I have a 35" spare in my cargo space, I put it where the back seat used to be. I strap down my tool boxes and spare parts behind it when I go 4x4ing as well as my small sub box.
I do not recommend putting a 80# tire on the roof, not if you are going to be doing any serious wheeling, the weight up there is not a good thing.
The absolute best place for the spare tire is on the back, the BII can use as much weight as it can get over the rear bumper and keeping it down low is a good idea.
The cargo floor is the second best spot.
What do you need to see out the back your side mirrors and rear view mirror wont overcome, even with a 33" back there, who cares! I plan to get my spare back on the hatch ASAP..
the 4.0L conversion is basicaly a bolt in affair, there is a bit of wiring that needs to be done, but its not too difficult IMO.
best upgrade you can make to this truck will be putting a 4.0L in it.
try doing some research on this and then come back with questions, I have answered the 4.0L OHV conversion questions about 800 times online, and I learned how to do the conversion myself by researching it years ago. if you still have questions or cant find all the info you need then come back and I will be more then glad to help.
Try this forum, therangerstation.com, rangerpowersports.com, google.com etc
This is a pretty common swap, but then knowing almost every conversion is different no matter how similar, you need to know 100% of what you need to do and why, transmission choice, how you wire it, what year 4.0L you use, etc all play a role...
if you are prepared enough and have a prebuilt wiring harness ready to go this conversion can be done in a single weekend