I hate to send you down the wrong path, so I'll just throw this out there. First off, which year motor are we talking about, I'm sure you posted that up someplace, but I haven't read all your posts.
When the guy did your motor did he swap the cam out? It could be any number of things wrong, but it sure sounds like your initial setup is wrong.
Having the sync sensor ( or cam position senor) clocked is important in OBD models. This is where it gets involved. It's possible the cam is out of time. Many timing chain crankshaft gears have two choices, some have a slot and you can adjust.
I'm beginning to think the flex plate or the cam is clocked wrong. If the cam is clocked (way) wrong it will often show up as low compression.
Pull the distributor and look down the hole with a strong flashlight, check out the gear teeth on the cam. Figure out someway to check that the pin (shear pin) going through the distributor shaft isn't broken.
Like I said, I hate to send you down the wrong path, but if I'd spent that much time with a motor and never gotten it right, I'd start over from the beginning. TDC 1, either verify it with a degree wheel and a piston stop or do it the old fashioned way with a curved piece of wire stuck down the spark plug hole and feel when the piston is all the way up, timing marks at zero. Now here is where you'll either hate me or love me, take the valve cover off, use either a dial gauge or another good way of measuring and check to see that push rod side of the cylinder one rockers are all the way down on the pushrod side and all the way up on the valve side and match in height, at true TDC (hopefully at zero on the timing marks).
I vaguely know how to clock the sync sensor, just what I've read, never had to do it myself. It seems to be critical on OBD motors. Check with somebody with the same year as your motor and see exactly where the rotor is pointing at TDC one. If the cam is timed wrong (wrong cam or setup wrong) the rotor and the sync sensor will never be right.
Like you said it may be your flex plate (sync ring) it may be something entirely different. Experience tells me it is likely to be the initial setup or something really simple that you are overlooking. At least it seems to be constant and not something intermittent.
If I took the valve cover off I'd also use a dial gauge and compare the height of all the cylinder rocker arms at the top and the bottom and compare. Especially if I had a new cam or lifters, Cams usually fail quick if they are going to fail.
You mentioned it seems worse when the motor was at operating temp. this usually indicates a sensor issue. Some sensors don't really come on line until the motor heats up. One sensor fails (shorts or partially shorts) and it can suck down the supply voltage to a number of sensors. The first sensor out of the envelope pops a code, but the sensor causing the grief may not show up as a code.
If this were a Renix I could probably be more helpful, I know them a whole lot better. I wish I was nearby, I'd stop in and try to help some.
I did live in Escondido for awhile, way back when. Most of the town was relatives, three Cops and twenty some bothers and cousins all in the same age group, we owned that town
. They are still probably telling the story of how we filled some asshat Cops car full of gravel (he was parked in a gravel parking lot). Only took a dozen of us five minutes to do, while he was inside the bar making "bull of the woods" noises. LOL I bet the next time he rolled up his windows and locked the doors.
