I agree please explain the wiring a little more from the sound of it, it was wired so that you could shut down the ignition coil from inside the engine bay. Maybe it was some sort of as CowboyPA said "Kill switch" like so you could park in a crappy neighborhood, and in order for it to get stolen they atleast couldn't drive it away.
If those are the only two things it joins, then it is realy unlikely that it has anything to do with your alternator issues(to be sure, take it out-in a short term trial sort of way). But your voltage issues could be so many things, do you have aftermarket audio at all, or other lights, or C.B.?
Chrysler did a s&^$%&^y job engineering the wiring on not just these but pretty much all their products.
'89 XJ Limited
[COLOR=Red][B]3"-4.5"ish Homebrew lift[/B][/COLOR]
[COLOR=White][B]16x8 MB Motoring Rockers[/B][/COLOR]
[COLOR=Red][B]265/75R16(31[SIZE="1"]ish[/SIZE]"X10.4") Goodyear Wrangler M/TRs[/B][/COLOR]
[COLOR=White][B]Trimmed w/ Bushwackers[/B][/COLOR]
[COLOR=Red][B]Stock 3:55 gears[/B][/COLOR][/B][/SIZE]
[B][COLOR=White]sans big audio[/COLOR][/B]
[B][COLOR=Red]Homebrew intake w/cone filter[/COLOR][/B]
"Some people are like a slinky... Not really good for anything, but you still can't help but smile when you see one tumble down the stairs." :my dad