Inconsistent, consistent missfire sr20det

[Dudreigez]

Hey everyone a fellow member suggested I posted my current issue up here to get some well needed advice!

The story -
First of all the car is a 1991 k series s13 with a sr20det (redtop) that has had a very recent rebuild. At the time of purchase it was running a standard ecu, 480cc injectors and standard afm. The car came with an apexi power fc and a apexi turbo timer kit with a MAP sensor. Initially the car ran reasonable and had a minor miss every 10 or so seconds.

Here's when the trouble started....
I installed the power fc with the map sensor and did all of the steps required for it to self learn idle and then took it to a tuner. The car ran fine with no misses however underload it would not rev past 5 grand and we noticed that the coil pack harness was not even grounded (how the car ran I do not know!) and it was shorting out on the tappet cover! Anyway we took it off the dyno and as I was driving back home on the highway and the car developed a miss on one too two cylinders. After messing with the harness the misfire went and I continued driving until it began again. So this time i replaced the apexi ecu back to the standard ecu and it ran fine with no misses for 3 days until the misfire began whilst the standard ecu was installed. This prompted me to start investigating the issues.

What I have done so far -
Identified that no. 1 cylinder is the one of interest. Initially I swapped coil packs with the no.2 cylinder which didn't solve the issues.
I then removed the coil pack harness and checked the continuity of all harness wires (signal, ground and power) and all were withing expected ranges), reground the harness and wrapped it in electrical tape to ensure proper insulation. I then reinstalled the harness with no prevail.
Changed plugs and checked that I was getting white/blue spark from all
I checked the continuity of the coil packs and all read 1.2 ohms. I might also mention that the do not have any cracks in them either. I should add that the car would occasionally run smooth and then return to a miss on cylinder one.
I then checked the continuity of the coil packs from the coil pack harness back to the ecu and all had similar continuities...
Running out of Ideads i then checked and cleaned the afm WHICH WORKED!!! Finally the car ran smoothly and did so for quite a while. However I turned the car off and started it back up to go for a drive and it started missing again.... EFF
I left it for a week because I was out of town to return to the car idleing fine, however the miss developed on cylinder one again after 5-10 seconds.
I should also add that I have tested for vacuum leaks with break cleaner with no prevail.

Where I go from here....
Check injectors
Potentially replace no.1 coil pack wiring.
The bolt for coil pack no.1 has been snapped off in the tappet cover and I was wondering could this be causing the coil pack to short or not be grounded???
Any help would be greatly appreciated!