Electical Issue?

'87 SI, injected. Problem started with voltage "idiot light" flashing. I replaced the alternator, ran fine on my hour commute to work. About 30 minutes into the trip home the interior electrical stuff started to shut down then the car quit. I sat for about 20 minutes she started right up and drove fine for about 10 minutes then same thing. I've now replaced the battery because it now tested bad (tested fine when I replaced the alternator). I've tested the ignitor and tested fine. The coil tested low OHM's on all three recommended tests, but it was not the recommended 70 degrees. When checking for shorts at the fuse block with a test light it lights up on both ECU fuses, condenser fan, rear defrost, sun roof, tail lights, clock, and brake light fuses also. Should some of these fuses have power to them all the time, like the clock and lights? Is there some common thread between all of these things that would cause them all to light up, or do I have some big fricken electrical issues?

Check your new alternator, I once bought a new alternator that didn't even last a week. If the voltage regulator in your new alternator is bad it could have fried your old tired battery. The symptoms you've described are typical of a bad alternator, I'd get another one. Also, don't buy the cheapest one and don't buy one from Schucks/Checker/Cragen, they're crap.

Took the alternator out and had it checked, surprise, it failed! Got the new one and will put it in this weekend. What about the fuses, does anyone know if the above listed uses are supposed to have power to them all the time or am I also looking for a short??

Most of the accessories you listed do have their own leads that are branched off directly from the battery, so I don't think this should be a major concern. You should be "good to go" once you have the new alternator installed.