My Setup: 00 TJ waggy 44's f/r waggy discs front waggy drums rear. All new brake components on the axles. Here is my issue, brakes work great just the pedal is very soft and travels way to far. Most likely from the increase in size of the caliper pistons and the rear wheel cylinders. My question is what MC will will be a good match for me, 98-02 Dodge 3500, E350, grand marquis? From what I have researched the 3500 will be the best swap, but I only read about it being used for f/r discs and on 3/4 and 1 ton brakes. I have yet to find a straight answer on this, will the 3500 be too much MC for these brakes? is there another MC that is a better choice? Any help is greatly appreciated.

I don't know much about Jeeps brakes specifically, but from the symptoms you described, I think you're on the right track adn you'll want to go to a larger bore master cylinder (or better yet, a quick take-up MC with dual bores, one big to pump up the system and then a smaller bore to create pressure) to move more fluid. That will increase your pedal firmness and decrease it's travel. Make sure that you have a 10# residual valve on the rear drums to keep the shoes close to the drum, otherwise you'll have a lot of travel. These are either integrated into the disc/drum MC's usually or you can use a disc/disc MC that doesn't have this feature and just add a stand alone 10# residual valve in line with the rear.

Not sure if this helps, but since you've got both Waggy axles and brakes (what year?), why not use a Waggy MC? You've done some research from the sounds of things so maybe you already know all this, but here's some info I had laying around:
1981-1983 Cherokee, Wagoneer w/PB....40.0mm X 28.6mm....ACDelco 18M217 (A1 Cardone remanufactured unit #101873 is $27 at RockAuto)
1987-1993 ""
Thats a QT MC with a 40mm (1.575") primary bore and a 28.6mm (1.125") pressure bore.

From what I have read the waggy MC is a lot of work to get it onto a TJ, also the dodge MC is already set up for drum/disc so it should have the correct residual pressure. But I am looking for someone that knows for sure.