Higher RPM missfire

I have a 98 that I have been driving about a week now. It had a blown radiator when I got it. It sat for 3 years. After going through everything it turned out I fried the computer. I installed a "new" computer from a same year/make/model/ sub model. I flashed the computer and figured it would run rough until the computer adjusted. After driving it for a week and idling a bit low 750rpm, but driving fine, the CL came on and it scanned a misfire cyl 1 and 3 and random misfire. I put my timing gun on it and it seemed that the misfire was worse at higher RPM. Didn't even see it at Idle. The spark was intermittent when I pulled the throttle back.

Before the CEL came on I installed new plugs, wires, cap, rotor, coil, t-stat, CAT, Muffler, and a CPS from Autozone(they were open). It seems the misfire is electrical since the timing gun showed intermittent spark.

Could the CPS not be sending a strong enough signal at higher RPM? I have not checked the Cam Sensor to see if the holes are aligned.

I have pulled and cleaned/sanded all ground connections prior to CEL coming on.

Thing runs fine, but would like to be firing on all the cylinders, all the time(or at least when they are suppose to fire).

Thanks in advance for your help. I did a bunch of searching, but the high RPM misfire I didn't see much on.

Cam sensor timing. Get out your toothpick!

sort of what I was thinking, but with the CPS being from Autozone, I didn't want to rule that out. I know where the holes are, but which holes need to line up. I heard there were a few.

If you search for cam sensor timing, you can find links taking you to full blown pictorials.