I put the rotors, calipers and pads from a 4 door on my 2 door tracker and after bleeding the brakes twice I still have a soft pedal.  Should I replace the Master Cylinder with the one from a 4 dr model as well?

When I got mine done I did notice a considerably longer throw in the pedal. I kind of expected it since the pistons on the 4dr calipers are bigger, but at 1st it was a very noticeable difference. I figured I would put a 4dr master cylinder in if/when the original gives out, but I've gotten used to the longer throw & don't even notice it any more.
If it's actually soft it's possible you still have air in the system. If it's just a longer throw to the pedal & brakes well once it reaches the right pressure... & doesn't sink, you're probably good to go. I've been running mine with the 2dr master for a couple years now & it's still holding up fine.

Hth,
Fuzzy

your description of longer throw is what I am experiancing now.  So I guess I will follow in your footsteps and run with the 2dr MC for now.

Local parts store list them at $170  Rock auto has them at $70

I was about to say define "soft pedal" - long travel does not equate to soft pedal in my way of thinking.

The most common cause of a soft or spongy pedal is trapped air, followed by binding or seized caliper slides.