Thanks guys. I made it back out the the shop this weekend and had a chance to play with the switch. Turns out, I did just have to back the rod out of the master cylinder quite a bit. I had put the new master cylinder on when I only had the chassis finished three years ago. By the time I added the aftermarket tub (with the firewall angle slightly different), and the draft pads both my clutch and brakes were too tight and had to be backed off.
Imagine my suprise when I tried to pull my jeep out of the shop after a year and it wouldn't move! The engine started just fine but when you let out on the clutch nothing moved. After a brief fit (maybe not so brief) I crawled under the jeep and saw the clutch wasn't releasing all the way..

I readjusted the clutch and all is right with the world.