Okay, tires are the factor that dictate what could be the "ideal setup for" : suspension lift height, CV driveshafts, gearing, axle shafts, brakes, etc. I agree with IMPED that more investigation/knowledgebase is needed to make the appropriate modification plan.
If i take tire size out of the equation for a monent and look back to the basis for my problem, How could i get clearance under the vehicle, now without a tire change? Without tires i can't get anymore clearance to the diff's. I assume that anything 3" plus suspension will Require a CV change. From here i could go back to what IMPED stated earlier -
My next question is in regards to the Drive shaft angles? At what point is it not good to push them? I understand that extreme angles put stress on U-joints. So with the 1.25" BL and 1" MML, would it require change to the CV?
1) You should put a double cardan shaft near the top of your list. Even if you don't 'need' it, it's the 'right' way to do it. Don't push the u joints, you'll be sorry you did. A body lift has no effect at all on driveline angles, which is one reason a small body lift is a good thing. The MML has a small positive effect on driveline angles and maintains the factory relationship between the fan shroud and fan when combined with a body lift. A MML has no disadvantages and should definitely be done, especially if you want to raise the transfer case. If you can visualize the engine/transmission/t-case orientation along with the motor mounts and transmission mount, you'll understand why.
2) You can fit 35's on ~2.5 of lift with no issues. Go highline fenders and they will fit very comfortably with less. Tires don't dictate driveline angles. The vertical relationship between the transfer case and axles dictates driveline angles.....obviously. A guy running 4" of suspension lift with 33's has a higher driveline angle than someone running 3" of suspension lift on 35's. Conversely, the fella with 3" of suspension lift and a flat transfer case skid will have considerably higher driveline angles than the guy with 4" and the stock skid. He'll also have ~4" more at the belly. The amount the transfer case is raised over stock ~equivalent to suspension lift.....the transfer case is seeing the same thing. It doesn't know the difference.
3) I'm a fan of lower suspension heights and maximum clearance while being able to adjust to any changes so put a full set of adjustable control arms on the list too. With 2.5" of susp. lift, 1.25" body lift, and a Rokmen skid, I've got 17" under the belly. I'm making a flat skid that will get me to 19". The transfer case is seeing the same angle as ~7" of suspension lift. Personally, I don't feel comfortable running higher driveline angles than that on a SWB TJ. With more suspension height + a flat skid, I'd break that rule and the angles would be too high for my comfort. The CV would bind before full droop as well.
I know I'm getting in depth here so I just hope it helps you think. Once you realize how everything interacts, things will start to click. Let me know if you have anymore questions--otherwise, I'm tired of typing so much.