[KrisSmithRocks]

well the first thing that i would check is where did you buy your alternator... if it was schucks then take it back get your money back and buy one somewhere else they have a %40 return rate the shop i work at wont install them anymore because of warrenty problems... next check your base timing you mentiond that it was dead on but the most of the symtoms resemble timing issues. At one point a friend of mine did a timing belt on a car and after a week or so the car started running like shit... like the timing was off but when we checked it was dead on... what happend was the harmonic balancer bolt backed out and the bottom pully started to walk and eventually sheared off the key so that it moved... so looking at the timing marks everything lined up but if you compared the mark on the flywheel with the crank it was deffinately off. so just make sure that the timing is bulletproof... next i would check the ignition timing... Make sure that when the distibutor cap was put on they didn't screw up the timing... well those are my sugestions so far...hope they help...

P.S. On my integra the crank has 2 timing marks if you line it up with the one it says to in the manual it runs like shit if you line it up with the other one it runs just fine. good luck.