Brief 'check engine' light blink

This has happened twice in the past week. I was driving along and my check engine light came on for about 1 second and the went off. Specifically, it was when I started driving, just got on the highway, and was in second or third gear. In other words, it was my first time through the gears on my way up to highway speeds.

The symptoms (minimall)
-gas mileage in the low 20s. This doesn't bother me, I live 5 miles from work and all my cars have low gas mileage unless we go for a long trim.

-rough idle. Again minimal. You cannot see it on the tach. I can feel it because I try to pay attention to these things. Passengers have never been able to notice

Changes I have made in the last 3 months
-change to all synthetic fluids (previous owner used petroleum based) Just changed the oil last week and thought I overfilled it a little. Let that out the next day.

-K&N replacement filter

-tranny filter and cooler installed

-power steering o ring fix

-rotated tires and painted center caps

One of these two may be the culprit

-resistor mod two weeks ago (replaced the resistor after one day)

-last week, swapped ECUs from another '92. This one had the EPROM mod, tan resistor cut, and black one crushed. Mine had none of these.

So, the check engine light makes me fear impending doom. I don't know where to start to look. The car runs great. Any advice would be greatly appreciated.

Oh, nvrmore, did anything funny happen in the brief time you had this ECU in?

Thanks