Finally got around to buying a multimeter (which sucks, I'm going to return it) so I opened the hood to find the cause of the rough acceleration that I've had since the DC tour.
I was guessing that it was going to be a stuck lifter, but I decided to check the basics before I even pulled the valve covers off. I checked the impedance of all of the plug wires and this is what I got:
Cylinder #8 - 91.6 ohms
Cylinder #6 - 100.4 ohms
Cylinder #4 - 121.4 ohms
Cylinder #2 - OPEN!
Cylinder #7 - 152.2 ohms
Cylinder #5 - 127.5 ohms
Cylinder #3 - OPEN!
Cylinder #1 - 152.2 ohms
So I guess during the dyno run I had two open plug wires! I don't think that it would make a difference in hp, because at those rpms I'm sure the spark would just arc over the dead spot in the wire, without a problem.
I cleaned up and put some new terminals on these wires the day before the DC tour, unfortuantely I didn't have a multimeter at the time to check the impedance before I installed them. I just fixed them tonight, they both measure around 100 ohms now, I'll install them tomorrow. Hopefully that was the problem.