Ok...Sorry for the thread diversion
@Classic>New.
I kinda read through your original post again. You say you want 35's. That's awesome, so do I. I'm gonna warn you up front...it ain't cheap. If you want a rig that you can actually depend on when you're out in the boonies, anyway. If you just wanna roll up to Tommy Hilfiger or Hollister in your Jeep on 35's to look cool, that's a lot easier to attain.
This thread —->
LINK<—- is a decent place to start. Its not all inclusive and I haven't read it in a while, but there is a fair amount of good information there. There are nuances once you go down the path, but the thread will get your head right. I noticed you mentioned 3" of lift. You'll need a 1" body lift and probably highline fenders to get the uptravel that really makes for a good ride to fit 35's there. Doesn't sound like you're opposed to highlines, so 3" of lift should be fine. If you really want the cat's meow though...a 4" lift might be better. With a 4" lift, it is easier to fit 12" travel shocks and get that 6" up/6" down balanced travel that is desirable.
Buy quality components. I'm coining a phrase here, There is never enough money to buy right, but there is always enough money to buy twice. If you try to cheap out on a lift, you'll be going through and buying it again. That's not to say you have to spring for the most expensive doodad or gadget everytime you buy something, but when you're dealing with stuff like suspension arms, brakes, Steering, etc, get the highest quality you can afford.
Speaking of suspension, I won't tell you what type of joint to buy. I have Currie control arms with Johhny Joints and I like them. I haven't had any opportunity to compare them to anything else other than worn ass factory shit, so I'm biased. I will warn you against some of the joints that use a thread in shell to hold the bushing in compression (think Rubicon Express). As they wear, they will lose preload and the joint loosens up. A Johnny Joint won't do that, because the preload is set by a snap ring. That is the key difference between the Johnny Joint and EVERYTHING else out there that is similar. I suppose, eventually, the JJ will loosen up too, but from all the accounts I read online, the threaded ones loosen up much more quickly. Quite a few guys are running the Duroflex joint from Metalcloak and they like those too.
Axles...You have stock Dana 30/Dana 35 combo, right? There are a few options...all of them costly. First option...Super Dana 35 in the rear with a selectable Locker and Chromoly Axles in the Dana 30 with your choice of locker (either lunchbox or selectable). 4.88 is the highest ratio you can get for the Dana 30, IIRC. You talk to the guys that run in the rocks, and they say its all you need. I don't know...I'm in michigan and traction is kinda non-existant. The nice thing is that this option does not require any welding, truly a bolt in experience.
Next, you can try to find a TJ Dana 44 for the rear of your jeep and replace the Dana 35. Not a bad option. Still mostly bolt in. However, I think the Super35 combo comes out cheaper in the long run and its stronger than the factory Dana 44 axles to boot (both 30 spline). Basically, the regear and locker are a wash, so you're trying to compare the cost of new axle shafts and a carrier to the Dana 44 Housing. You can get the High Strength Axles for the Dana 44 too...for what that's worth.
Finally, find some TJ Rubicon Axles. This is a pretty awesome way to go, when you first think about it. But, if you think more critically, I'd reconsider. You still need to regear The front Dana 44 is more of a Dana 30/44 combo (the tubes, knuckles, Inner C's and stub shafts are the same between the two). You already have a Dana 30. The TJ Rubicon Lockers are decent, but not great. If they break, they are almost impossible to get parts for and they are very low pressure air lockers with their own independent air pumps. The pumps run about 5 PSI...so its not like you can just run an ARB compressor for them. So, that is another cost and sourcing problem. Finally, the axles are incredibly expensive IF you can find them. tThere are two really good reasons to go this way in my mind. One is that the larger ring and pinion allows for deeper gearing...which you don't desire. The second is that they will bolt in with no real Fab work.
You can also try to find a High Pinion Dana 30 for the front. Kinda neat, but not really necessary.
Next we get into major Fab...so I won't detail it much. You can use a Ford 8.8. Meh...I think this was a really good option on YJ's with the leaf springs, but there is so much fab work involved to put them under a coil sprung TJ, the benefits don't justify.
JK axles. Supposedly, these are stronger than their equivalent TJ versions. I don't know all the details, but I do know you have to cut all the control arm brackets off, weld on new and figure out steering (TJ to JK is different styles of steering). You also need new wheels (different bolt pattern and brake clearance) and the Axles are about 5 inches wider than TJ, but some of that is used up in the shallower offset of the JK wheels. Lots of work, but some decent benefit. Personally, if I were contemplating an axle swap, a pair of JK Rubicon axles with electric lockers kinda tickles my fancy...but its a TON of work...and they only come with 4.10 gears, so unless you find a set already set up to what you want...you still have to pay 1200 bucks for a regear.
Interior stuff? Do that whenever you want. I've upgraded my stereo and installed seat heaters. Creature Comforts are really nice in a daily. I think some more sound insulation and a hard top would also be necessary for DD duties.