Ok, I have a 94 EX with D16Z6, 130k.

Mods: MSD Blaster II external coil, with MSD power cap and rotor, Accel 8.5 thundersport wires, NASCAR NGK V- plugs set at .044, and Short ram air intake.

I did the coil swap myself, and the car had no problems untill a few days ago, it misses randomly, and if its in a high rpm (1000 or higher) it does not miss as often, and if I am driving, and put it in 1st, and take off (normal driving), then it does not miss, it seems like if there is a load on the motor, then it does not miss, but if there is no load, and it idles around 350-500 rpm it misses randomly, not enough to kill the motor, just enough to sound like shit. My exhaust has not color to it, and smells a little gassy. Also, when I wired the MSD Coil, I took the + and - leads off of the internal coil (removed the internal coil) and ran them to the external coil. But when I got a new MSD cap, the diagram shows me taping into the wires from outside the distributor, and I was not sure if that would work correctly, since, there is a small (resistor type box) that one of the wires come off of, and I dont want to bypass somthing and end up frying anything... Can I bypass this box, or remove it if I am using an external coil? Also the small resistor type box says (Hytachi), but when I order a cap I use a Tek cap? I am almost positive its not the coil, but I am not 100% sure its correct.
(just recently replaced plugs, wires, cap, rotor, and coil)
Plugs are set at .044.

I dont burn any oil, and the plugs look normal.

My next rout is fuel, I am not sure how everyone elses car starts up, but when I have a full tank of gas, my car seems to turn over and start much quicker then if I have 1/4 or less, it seems to crank over one or 2 more times, when I am low on fuel, could this be a fuel pump problem?

Also I am going to check my timing today, and I will see if that helps anything. What is the timing suposed to be set at?

I am going to check my valve lash as a last resort. (what are my Intake and Exhaust valves suposed to be set at im MM's (.00?what?)

And I am positive I have good grounds, just recently replaced grounds, and I also have a brand new battery, and my charging system has never given me any problems.

Other then all of that, is there anything else I should check for?