Been awhile, but wanted to report that the jeep is now running good. Turns out it was the wrong coil. I ended up taking it to a local shop and they determined that it had a coil requiring an external resistor (which I don't have), so installed a coil with internal resistor and it runs fine.
The gas color issue went away, so it may be that the new filter or fuel tank had some coloration that eventually cleared out.
Now I have a noisy 3rd gear to work on and some chatter in the rear end when making a tight turn....oh well.