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Yea, I did the heads with the engine in the car because I was doing the job away from home and was trying to do it cheaply as possible for the girlfriend. Turned out to be a loose ground on the intake manifold. I'm guessing I forgot to tighten it the second time I put the intake manifold back in. Thanks for all of the replies and getting me on the right track. Now off to figure out the slight misfire issue...

I'm guessing you are referring to B20, B21, and B22. I'm guessing by looking at the diagram that B22 is the culprit. I did wipe off some grease on the wires going to B19 because it looked like that bundle needed some electrical tape. http://jdmfsm.info/Auto/Japan/Subaru/Legacy%20Outback/1998/Service%20Manual/WIRING%20DIAGRAM/WIRING%20DIAGRAM/MSA5TCD98L21378.pdf As seen on page 129.

Thanks, I'll give that a shot. I think you are referring to the ones that are just behind the engine more near the bellmouth of the transmission, correct? I didn't disconnect any of these, but maybe they got jostled in the process.

I replaced the head gaskets on a '98 Legacy Outback with the EJ25D engine without removing the engine. The engine fired up immediately and ran great. I ran it for awhile then shut it down to check the fluids and give it a good looking over. Upon restarting, it sounded like it was misfiring and the CEL came on. I thought it was the ignition wires as I had reused them and had one that was questionable. I replaced the wires and took it for a test drive. The transmission seemed off as it was shifting hard and erratically. But it seemed driveable, so I tried to get it to a store to hook up a scan tool. It cut off after the AT Oil Temp light came on. It wouldn't restart. The temp gauge went high and the fuel gauge went low despite there being a full tank. The indicator lights on the dash didn't seem like they were doing their normal startup routine either. After trying it to start it a few times, I decided to check for spark. Before I did that, I noticed that the gauges went back to normal. It started right up and then shut down shortly after. Afterwards the gauges went back to haywire. Now, the dash lights stay on after the key is removed and sometimes the AT Oil Temp light flashes after the keys are removed.