Miss at idle, miss at cruising speed.

NA and Vin 7 plates are different. Different balance holes.
These are the most common numbers that may pertain to Mr. Helwig's specific inquiry, but there are a number of additional flexplates not specifically listed here.
YearVIN CodeGM PN*Pioneer PN
198619877 (turbo)25512350FRA-147
This issue started after the engine was removed for a rebuild. Just a stock rebuild, nothing fancy. The engine has always seemed to have a long crank before it fires but it was doing that before the rebuild. So the problem is a miss at idle that shakes the engine, its not a dead miss as it comes and goes in a strange rhythm. Its there at cruising speed, the whole car shakes, 55mph is about as fast as you can go....feels like something is going to break. So to me it only does this at closed or near closed throttle as it runs great when you put the boost to it. It also never puts out a code.
Here are some of the things I have done/changed
Fuel pump hot wire w supercharged buick pump in tank. (fuel pressure is at spec, mine is adjustable. It comes up at key on and rises with boost)
Replaced injectors with stock Delco units
TPS (set to spec)
Delco coil pack
New ignition module (Ive put 3 different ones on, no change)
Stock Delco plugs & wires
Delco ECM with Caspers ECM pigtail kit (stock chip I think, I have another one the says Street Thrasher but no change between the two)
New crank sensor
New LT1 MAF/translater setup
Bosch single wire O2 sensor (I have 3. No change)
I am a licensed technician in the trade for 26 years now so I can say I have gone over everything with this car. I've owned it 22 years and it drove great (13.6 @99) until the engine was removed for rebuild.
I don't have a scan master or powerlogger yet. I have been using my 1980s vintage Snap-on "brick" scanner. I've read and reread everything on this site plus vortechbuick......I've read it all!!
As for scanner numbers, everything seems right, my BLMs at idle are around 128, the O2 is switching, coolant temp is normal.
I removed the intake so I could look at the camshaft and liters.....no problem there. I did compression tests and cylinder leak down tests.....nothing found.
I've checked all powers and grounds involving the ECM & C3i module, I've even scoped the cam & crank signals.
This miss is not on a specific cylinder as removing an injector plug causes the engine to stumble on all cylinders equally.
Now yes, I have not changed the cam sensor, I have removed it about a hundred times and it is set properly (no side to side play, I did adjust the up & down play)
One thing that I find strange is my tach reads about double what engine speed actually is. I know its not correct but the scanner reads about half that and thats what I assume the ECM sees. I think the gauge is bad? Do you agree?
I've smoked the intake and exhaust...no leaks. I have removed and plugged all vac lines except for PVC and brake booster(it was converted years ago). EGR has been removed and plugged.
The engine has this strange shake. If i take if off idle it will shake more and you can hear this cough sound in the exhaust. Is it possible that it is going in and out of sequential mode? Im lost, and it is dragging me down.......Please help me

Is far as i can tell
I would remove the balancer and have it checked for cracks. Could cause a balance issue and a miss.