So over a month ago I was driving my 98 Lego and the alternator and brake warning lights came on. I had a road trip planned so I went and bought a rebuilt alternator and new belt from NAPA and swapped it out. I am still getting the lights intermittently, although the battery hasn't died or anything. I put a multi meter on and have about 12 V when off, 13.5 when running, and just 12.1 when the warning lights are on and running. My question is did I get a bad rebuild or is there something else like the battery that could be causing this?

Output from alternator is low. Should be 14 volt output. I think you got a bad rebuilt. Does your NAPA store do charging system checks in their parking lot with your car parked outside?? It needs to be checked out.

$hit rebuild. Get a reman from Subaru. It's both cheaper and better quality. Due to a recall back in the 90's the Subaru dealer reman units for those cars are like $70. 

GD

I once went through 4 different parts store alternators before I finally got a good one. 

I would of went with a Subaru one but the closest dealer was 50 miles away in the wrong direction. 

I got lucky and got a good one from junk yard $40.00. I had alternator re-builder  bench test, which he did not want money but I insisted he take something. Make sure you get the right alt., there is differences. I dont remember what the difference was but my rebuilder told me what to look for, & I think the junk yard had a cross over listing as well.