So my head started to lift under boost right after we tuned it. So I went ahead and replaced the HG and threw in some ARP studs. Setup is stock LS motor (b18b)

After the HG/HS install, I started it and it sounded like a WRX. I could tell one cylinder was missing. Checked them all by pulling the plug wires with it running and it was cylinder 1 (closest to the Timing belt)
I thought it was the plug. Bought a new set of bkr7e's and gapped them down. Still missing at idle up to 3k rpm's, but runs awesome 3k and above, no breaking up even in boost. (smokes the tires in third :D)
So I figured it was the timing. Checked it with a timing light, and it is spot on.
*****Buttt....on cylinder 1 and cylinder 1 only, the flashes from the timing light are not consistent. It will flash consistently, then stop for a second then start flashing again. Check every other cylinder with the light and the flashes are evenly spaced and don't ever stop (the way it should be)

Okay so I replace the plug wire on cylinder #1. Still does it.
Okay I will buy a brand new set, possible two bad wires. Still does it.

Replaced the cap and rotor. Still does it. Checked it with another plug wire on cylinder number 1, still does it.

Maybe its the mechanical timing? Nopeee-- I just re-timed the motor and used the cam fixtures, so no way that only one cam is off by a tooth. And if the mechanical timing was off, it would show up with the timing light. (the 16deg BTDC mark wouldn't line up with the pointer on the T-belt cover.

The onlyyyyyy thing that is bugging me is not having the plastic cover on the distributor, the one that goes underneath the rotor and covers the coil. But I'm stumped because if it is somehow arc'ing out inside the distributor, it would do it all the time, and possibly on more than one cylinder. The car ran fine with the motor the way it stands before the HG install.
Also, like I mentioned, the motor runs perfectly in boost and upper RPM's, and it's not like it's really running on three cylinders where you have no power. Even down low, you can just hear it slightly missing, but the power is still all there.

Help me out I'm going crazy.

 

could be the beginning of a distributor failure...any weird dancing going on with the tach? sticking at rpm or jumping around?

had a toyota in my shop last week...same thing, misfire at idle ran like **** until 3-4k and then it ripped...bad ignitor in the toyota's case...I've seen similar problems on honda dizzy's as well...usually the ignitor or the coil or both...try swapping a known good dizzy and see if the problem goes away