On the gearing issue I ran the BOM numbers on my axles and they came with 4.10 gears. The research I have done indicates that in 2004 manual 5spds came with 4.10's and anuto's came with 4.56's.
Can you verify it with an actual turn count or even better a look see? The D35's are called C's because they come from Dana unfinished. I forget what gets done to them at Jeep, offhand though. Since 2004 was a minor change, it's really hard to tell without actually looking at them. You get a lot of weird things that aren't official in transition years as well.
Case in point, in 1995 all the 4.0L's were going towards the XJ and ZJ. This is why there were very few 4.0L YJ's in '95. What most don't know is that the 3.73:1 geared axles were going towards them as well. So you sometimes get 2.5L Auto's with 3.07's.
I can't imagine turning 35's with 4.10's really well though. I turn 35 with 4.56's and its OK but not great.