I highly recommend - going here and reading, don;t start off by asking a question, search and read a lot.
http://www.pirate4x4.com/forum/forumdisplay.php?f=12
and
http://www.pirate4x4.com/forum/forumdisplay.php?f=16
they aren't the nicest group, but the content they provide is actually very good
they believe there aren't stupid questions, just stupid people that ask questions
Lots of guys who run mud don't see the need for 4:1 or 5:1 TCs (a doubler may work if you also need a real tall crawl ratio for other types of wheeling you may do)
If you cut the fenders and the quarters you will not have to go as high and you will not need to change your drive line angles as much
the higher your suspention goes the higher your drive line angles get and the more you have to do to fix them
your tire size will dictate your true clearence at the diffs so go as short as you can for the tires you want.
One of the big items you didn't mention was the brakes. Stopping big meats is tough (and yeah - 35s are getting up there in size and weigh a ton). turing will be affected as well. you want to make sure your tires don't rub and stick when turning from lock to lock
buy some extra used shafts as wheel it until they break, then replace.
all your questions are good.
alot of the answers depend on what you plan on doing with the rig
The type of mud you run makes a difference too, rutted mud trails i like to see tall and skinny tires, mud pits and mud fields, i like wide tires. On the trail- you will be able to cut deep enough to find hard stuff for traction, wide tires keep you on top of the real thick deep muck stuff.
as far as gears go, don;t go stick 4.88s in if you already have 4.56s. you are tlaking less than 10% difference right now. You may eventually want to go to 5.29s but you don;t want to have to do it if you do swap rears and do a SAS up front sometime in the near future.
vent the diffs and trans well.