Jeep Strokers

Hey guys, been meaning to do a write up for a while now, this site and the feedback has been a huge help and inspiration for a while now and with much research on here I have finally built my own 4.6 stroker and is currently running in my daily driver. I've only got about 3000 miles on it and from the first start its been running well.
However I have been consistently troubleshooting a misfire issue, it sometimes comes up for a specific cylinder misfire but usually with the random misfire code as well.

I am trying to get some more information about adjusting the cam position sensor with a DRB scanner. My understanding is that even setting the cam sensor on TDC, it can still be slightly off and that the DRB can zero it in or marry its setting with the computer and also the crank position sensor. I've talked to one jeep shop that had some experience with a few stroker installs and they said that they finally found that having it set at the dealer with the DRB got rid of the random cylinder misfire CELs

So I'm just trying to get a little feedback from anyone who was able to get to the bottom of this issue, I try to never go to the dealership unless its something absolutely out of my control. Ive found some sites that rent the DRB also. I know the next question will be the build of the stroker so with out going into too much detail ill just list the basics
2001 Cherokee
4.2 rods and crank
Sealed Power H802CP pistons
Block has been bored .030 over and decked .011
stock cam
0280155784 24lbs injectors
0331 tuby head and valve job done
I cant remember what part number the plugs were but I went with the next heat range cooler
I have tried swapping the coil rail with a known good rail (no difference)
also am running on 93 (tried 87 and it did not like it, probably from the larger quench)
Checked the fuel trims with a scanner LT trim is around +10%, ST trim usually around +2% (was much higher before going to the larger injectors)

any news on this issue? My new stroker only has about 200 miles on it so far and I've experienced a little stumble on occasion. Only happened a few times and don't get a misfire code. I also saw a post about the DRB scan and quick adjustment of the CPS to zero it off, but also something that has to be done at a dealership?

So I finally got a chance to have someone hook up the jeep to the DRB scanner. And i believe for the most part the dealers are the only one with them they have the ability to re-flash the ECU depending on different jobs that are being done the guy told me they had an update for the ECU that they would do when doing that fuel injector insulation mod and things like that.
When I looked at the scanner I could see that the cam and crank sensor were "in sync" so the mechanic didnt think the timing or cam sensor was the issue.. but I was able to see the misfire counts and sitting at idle I could see the number 3 cylinder just missing and racking up the counts but then as I brought up the RPM it seemed to smooth out and wasnt missing. So that helped me narrow down my issue and focus on the number 3 cylinder.

So far I have not been able to figure out why, as far as troubleshooting goes I have checked the cylinder compression and checked to see if there was any issues with valves leaking this all seemed to check out fine. I swapped spark plugs/checked the plugs and made sure the number 3 plug was actually sparking. I swapped fuel injectors and also checked the fuel pressure at the rail about 50 psi. I pressurized the intake manifold and soaped everywhere looking for a vacuum leak (did find a small leak at one of the sensors on the throttle body and fixed that but still no change), still a slight stumble at idle. But after doing all this the check engine light came up as a random cylinder misfire so i need to reset computer again and verify that and maybe see if i can get my hands on that DRB scanner again to see if anything changed after messing with things.

Im running out of ideas and not sure where to go from here. I just got a bottle of octane booster I thought as one more test I could try that to see if possibly with my build the 93 octane ive been running just isnt enough.
One thing that I suppose i need to check now also is the valve lift and make sure there is no issue with a cam lobe. The motor now has about 5000 miles on it.

Any input or suggestions would be greatly appreciated, Thanks