ANYONE that knows their SR20's

[luke91]

I have a blacktop S13 SR20 in my '91 240.  I finished the swap about two months ago, and have been driving it ever since.  A couple nights ago, I was driving home from a friends house, when the car completely died.  Nothing worked.  Not even flashers, or lights.  I pulled over, and just as I did, the battery terminals exploded (in the trunk).  I disconnected what was left of them, and called a tow truck.  
The next day, I surveyed the damage, and noticed that the battery cable (+) was totally melted, as were the terminals.  I also determined the cause of the short to be the connection to the positive side of the alternator.  The nut holding it on had come off, and it must have grounded to something else.  I screwed it back on, and replaced the battery cable with some thicker 2 gauge.  I checked all other wires and grounds to see if they had fried, or came loose.  Everything seemed fine, so i decided to put it on the road again.  Here's where it gets interesting...
I drove approximately 15 miles to a friends house, got gas, and drove another 15 miles to the local racetrack.  Everything seemed fine.  As I was parking, I noticed that the engine was idling on three cylinders, but when I gave it gas, it cleared up.  I thought this was weird, but thought nothing of it.  When I left, the problem was still happening, only now it was worse.  After about 5 minutes, the car was running on three cylinders, and would not clear up.  I pulled over, disconnected the battery for a few minutes, and looked under the hood.  Nothing was out of the ordinary, so I hooked up the battery, and hit the road.  Everything was good again, although I would feel an occasional misfire every once in a while, which is still out of the ordinary.  By the time I got to my house, it had gotten worse, but not to the point it had earlier.  
The next day, today, I drove out to run a few errands, and everything seemed fine, until the car warmed up, then it started misfiring again - bad.  It would consistently run on three cylinders, and sometimes even two.  I shut it off, disconnected the battery, and  waited a few minutes. just like I had the night before.  When I reconnected the battery and tried again, it still ran on on only 3 cylinders.  I have absolutely no idea what is going on here.  I think I might have damaged something when everything shorted out the other night, but I don't know what.  
The misfire sounds exactly like hitting the speed limiter.  Only it happens at all RPM's, in all gears.  Sometimes the car will straighten out and run on all four cylinders, but only for a few seconds at a time.  I don't get it.  Anyone that can help - I need it.  Thanks
--luke