check the bulbs first to make sure they are the correct dual filament style. after that I would check the connector in the wire harness located right behind the drivers side rear tire. I had some corrosion problems in there that stole my brake lights.
I do believe WJs have a 5-on-5" bolt pattern (your MJ is 5 on 4.5"). used WJ arms are fine to use. try car-part.com for junkyard searching :thumbsup: I paid $30 for my pair. but they aren't all that necessary if the rims do in fact have 3.5" backspacing. that takes the tires away from the arms and puts them into the fenders.
31s on factory jeep rims can fit a 4x4 MJ with minimal contact on the control arms. :thumbsup: they should clear the fenders entirely (it is a tight fit though).
WJ lower control arms have a bend in them and will clear the tires. or you can adjust the steering stops. or you can simply not crank the tires over quite as far.
car-part.com can help with finding junkyard axles. :thumbsup:
and I recently got another 44 for all of 89 bucks. they are out there. :yes:
U-joints don't like changes in their operating angles so you might be changing them in the driveshafts (especially the rear).
EPA aside, the can is there to absorb fumes that escape from the tank and removing it can result in a gasoline smell since those fumes will be escaping one way or the other. :thumbsup:
don't put any money into regearing a dana 35 rear axle. go find an MJ/XJ dana 44 or XJ 8.25 or Explorer 8.8 and invest your money into an axle that will last. :thumbsup:
likely the ratio in the axles is 3.55 (most common ratio found in a 2.5L/4spd stick). the trans would be an AX-4.