Just a hunch but at a minimum, you've likely got a grounding problem at one or more of the outside turnsignals. Try removing the lenses and removing the bulbs at each corner and leaving the sockets hanging with no bulbs in them...my guess is you'll see the problem immediately as corrosion in the bulb socket. Turn on a turn signal and try putting a bulb in that side and see if it works. If its not flashing, start look at the ground wire for that light. IFix the turnsignals before you try tackling all the other stuff that might be wrong. Keep it simple and work on problems you can get to easily first. You just might get lucky and solve some of the other problems with correcting the turn signals.
99 TJ, AX15, 2"BB,
99 XJ, AW4, 2"OME,
98 XJ, AW4, 2"ACOS/JKS Shackles