I just built a custom one off harness for my car, so since it's still some what fresh in my mind, hopefully I can give you some things to look for. I always start off looking at the grounds first. If I was to guess, it would be the wiring to the cam sensor. That area after 30 years imo is the weakest link with the harness in terms of reliability.
1) At the ignition module, check pinout L and G. Both of these are grounds. L is a ground to the cam sensor. G is a ground for the crank sensor (you might also want to wiggle the harness at the cam sensor and the crank sensor while the car is running to see if the problem gets worse. Wires tend to fray under the loom and finding them can be tough)
2) At the ecu, Pin out B12, D1, and B10 run your critical grounds from sensors to ignition.
3) Check the grounds at the back of the intake or head. Make sure that the 3 or 4 wires connected to it are all intact. Best to see on a hoist looking up near the dip stick tube of the transmission.
4) Check the ecu pin outs that the wires going into the ecu are all down. Sometimes when connecting these harnesses you will notice that a couple of the wires at the ecu connector will pull up and not make good contact with the ecu. Look at them all carefully and if you see one up, manually grab that wire and push it back in.
5) Did you check to make sure that the pump is supplying the motor with enough volume at the rail with a gauge on the windshield? The problem you have is either ignition or fuel related, whether it's in the electrical or hard parts. I know you guys have checked a bunch of stuff, but it would definitely be something to check.
6) If you have a stock ecu in the car, check the hose from the turbo to the mass air that there is no leaks in that area of the hose/pipe.
7) Check your fusable links at the starter. Those also share 12 volts for the ignition module I believe.
8) Check for any corrosion or bad wires near the ignition module and ecu pin out from moisture
9) Check your fuel filter and see if it's good, or replace it. Also it wouldn't be a bad idea to dump the gas in the car and get some new fuel and put in.
10) would be to inspect the injector harness for bad pins or bad connections, even replace with a known good one as another process of elimination.
11) Check your spark plugs and make sure the porcelain didn't crack when putting them in.
12)Last thing I have in my mind to check is the fuses under the dash for good connection and any piggy back additions that you may use the fusebox + voltage for.