I don´t know the ODB I, as well as earlier models, the computer power supply, may start, at the fuse/relay box in the engine compartment, along with some fusible links (inline fuses). I´d do a real close visiual inspection, before I changed any fuses, unplug the computer. Having the alternator bench tested, might be wise, be a bumber to get it all together and have a runaway alternator cause an instant replay, though that´s probably not the cause. Probably a short in the wiring, a wire rubbed through (on a piece of sheet metal) to ground, if the computer smoked, the connectors may be melted.
The only time, I´ve seen the computer smoke, was from a reverse polarity jump start, burnt out the computer and the CPS on an OBD I XJ.. Your old computer, may still be OK, even if the battery polarity or currect flow, was reversed (maybe) or a wire shorted.
I´d systematically, check every connector for melt down, a visual check on all exposed wires for rubbing and or contact with hot parts. And take a real close look at the fuse box for melting. Pull all the relays and look close at the sockets for melting, after a good visiual inspection, changing the position of the same number relay, may produce some results, all of the relays, are not interchangable. Be careful with the connectors, they get old and brittle and many have different kinds of retainer/locking systems. A burnt (open) fuse/ fusible link, may tell you which sub system is the problem, if you have a schematic. Might cut the possiblities down some. I keep an extra wiring harness in the shop, it´s often easier to follow the wires through the harness, on the shop floor, than try and figure out the schematic. Strange process but it works for me.
The master cylinder for the clutch, has a nasty habit, of leaking brake fluid onto the inside fuse box, a serious mess and sometimes shorts.
Electrical troubleshooting, takes a system, a book and a lot of time. Arn´t usually many shortcuts. You have to isolate/segregate the main cables, the components and sub-systems and test for short to ground. You might get lucky and find the problem with a serious systematic visiual inspection and a flashlight, if it´s somewhere visible. Electrical troubleshooting, doesn´t take anymore time, talent and/or patience, than a video game, but not nearly as much fun. :badpc: