Yeah, the Rubicon axle would need a factory air pump to run correctly. But that's not stupid hard to do. And if you can't find a single pump on someplace like Ebay, you have to buy the set of two (one for each axle) in the factory bracket because it's only sold as a complete unit new. And those run over $200.

And I forgot about junkyard parts for a disc brake conversion. That would certainly be cheaper.

As far as the strength difference of the D44/8.25/8.8, the differences between them isn't huge. They're all within probably 5% of equal strength between them. If you have one, there isn't really a compelling reason to switch to one of the others because you don't gain much. Upgrading from a Dana 35, you can't go wrong with any of the 3. If you want a lot more strength than those three you have to start looking at the Dana 60 or a built Ford 9". Or tons. And that means either a lot of custom fab or buying an aftermarket axle assembly.

 

I just had 4:10s installed. For a few reasons. 1st i did not want 33s. Mainly a DD with some off roading. 33s are a bit expensive. But with 4:10s I can run 31s now and if i choose to go to 32s i only need to change my lift or flares. The 31s really ride better than the 30s. Gas mileage is as good or better. After having 4:10s installed, driving home on the 30s gas mileage might have been 14mpg .I clocked the Speedo with the wives rav4. She was doing 70 i was doing 80. Had the 31s installed the rav4 was doing 70 and I was doing 75. Mpg came up to 15+ to 16+. Still breaking in. So I think if I go to 32s Speedo would be correct. Gas mileage may stay the same or improve a bit. I know I will be adding weight and mass with 32s but the engine will be running more where it likes to. But that is down the road.

 

I'm also running a 99 auto. Having regeared to 4.56 I've run 31 duratracs and 33 nittos, and up to 32 Kevlars on stock gears.

With out a doubt I say go to 4.56s. The desirability is still there, good pep on any tire size. 31s were fun as it felt weightless kinda. 32s and stock 3.55 was very noticeable on power reduction. I say go 4.56 f9r this reason, especially if your having the work done, cost to performance i.m.o. will not be had with as small of a jump as 4:10s.

Myself I went with use standard gears. They are cheaper but work fine. They are the same as Yukon gears without a little more warranty time. If you want any Traction device do it now vs later. Shop around for prices, but anything that's in your budget, you'll not find a difference in spending more here.
Don't skimp install, refresh everything with master install kits.



Now gas mileage, not a big variance between Stock and 4.56 on any of these tire sizes, the 4.0L is not a good motor for mpgs, other wise its great. 4.56 will give you pep, higher rpm highway speeds, but smoother transition of speeds, meaning turning and natural gear based deceleration becomes more manageable for the vehicles bigger tires = lil better mpg, but not a lot. No miracles here friend.



Best of luck on your choices!

 

I have a '99 auto as well. It sits on 32" Cooper STT Pros and has a bunch of weight added with front bumper, rear bumper/tire carrier and a roof rack.

I drive it to work occasionally. Also 2-3 hour drives to campsites/hunting/fishing/trail spots. It isn't towed.
I went with 4.10 gears and Detroit Truetrac front and rear. Feel like the thing rides perfect on the highway/freeway. I'm pretty sure I'll be happy with it even if I for some reason go up to a 33".
I searched thread after thread of this debate and usually most recommend 4.56. I thought about it, but ultimately went with 4.10s and don't regret a thing. It works for what I use my jeep for and I think 4.56 might be a little much considering how much highway this thing sees. (I'm usually driving 70+, and the thing rides smooth up to 80.)

If you don't do much highway driving and stay below 65 majority of the time you can't really go wrong with 4.56.

Drove my dad's '95 with stock gears and 31's quite a bit and switching to mine is like night and day. He also has the lunchbox up front which steered me away from that. Just wasn't a fan of the clicking in the parking lots or U turns.

You're gonna like either upgrade though. Just go with one that fits you more and if you're still unsure...there is a reason people say 4.56.