I agree with geeteeohguy & BearGFR that is does sound like a timing issue. However, my experience with a really retarded distributor timing is that the engine will heat up really fast on you - you can watch your temperature gauge climb. You did not mention that you experienced this problem?
I know you have double & triple checked everything, but lets run through some basics just in case.
First, have you observed the rocker arms with engine running to make sure nothing obvious like rounded/worn cam lobe? No rockers have fallen off or gone sideways and bent a pushrod?
Roller cam or flat tappet hydraulic cam? Assume flat tappet?
Firing Order - Counter Clockwise
on a Pontiac. 1-8-4-3-6-5-7-2
spark plug at the distributor cap should be at the 5 o'clock position as you look at the distributor from the front of the engine - or pretty close to it.
What do your plugs look like when you pull them? Wet, fouled, metal flecs, etc.? Correct heat range plug?
Do you have a new harmonic balancer? The outer ring is bonded to the inner section and on an older balancer, it is not uncommon for the rubber to deteriorate and the outer ring to slip - giving you an incorrect timing reading. And, make sure that harmonic balancer bolt gets torqued to 160 foot pounds or the collar that goes onto the crank can crack/break.
Does the engine have the 8-bolt water pump or later 11 bolt pump. Each has the different timing cover and needs the matching harmonic balancer. There are 2 sizes of balancers with the 8-bolt water pump cover using the smaller diameter. If it was swapped over to the 11-bolt cover and the smaller 8-bolt balancer was kept, timing marks on the balancer will not match correctly the timing scale on the timing cover.
Noted you have done a Pertonix Conversion. Needs to have the correct air gap. Needs to have the correct matching coil, and you need 12 volts
to it. The 1966 uses a resistance wire for points and drops the voltage to 9 volts while engine is running. If the key has been left on for any long period, I have read that this is one of the biggest reasons why the Pertronix conversions failed on their earlier units. They have supposedly corrected this on later versions.
Stock manifolds - does the manifold still have the "butterfly valve" with bi-metal spring? These were used to send hot exhaust gasses through the intake manifold exhaust crossover for faster warm-ups in cold weather. As the engine got to temp, the bi-metal spring opened up the valve and exhaust gasses exited as usual. If it is frozen shut, it'll cause problems and choke the engine. Exhaust pipes not damaged or plugged along its length?
What intake? Noted the Holley and swap to the Edelbrock (AFB?). If using a stock Q-jet intake manifold with these carbs, you would need an adapter. It has happened where the adapter was hanging just enough over the edge, but not really visible, to cause a vacuum leak because the gasket did not seal as it should have. The best intake is a dual plane and not a single plane intake. The single plane intake, if used, can be problematic at lower RPM's.
Have you checked fuel pressure at the carb? Could be a fuel pump, air entering the system via a split or bad rubber line, the sock on the tank's pick-up tube plugged up, wrong style of gas cap (non-vented vs vented) not allowing the gas to be drawn from the tank, kinked line, plugged fuel filter.
9" of vacuum is very low and indicates a fairly radical cam, but indeed may be the overlap in the cam. The factory cylinder pressure for the 1968 GTO 400 with 10.75 compression is 185-210 PSI @ 155-165 RPM's. Overlap on the "068" GTO cam is 63 degrees. I know that your cam has more overlap, but that cam will be poor down in the lower RPM range and won't perform at its best until you hit mid-upper RPM's. So if you have a stock torque converter or running 3.55 gears or lower - that engine will be bucking. With a radical cam more on the side of a race cam, you need a high stall converter and most likely 3.90 gearing or better to work with the cam.
PVC valve hooked up and working?
If you have power brakes, they may not work so well with 9" of vacuum. If you have power brakes - I would also check the check valve that comes off the hose from the carb/manifold that goes to the master cylinder brake booster just to make sure it is not bad and sucking air. This has happened to another member here and was causing problem. Valve appeared good and seemed to work, but it was worn out and not working as it should.
Lift on the valves? Any chance they are hitting the piston tops? Springs matched to the cam so the valves are not bouncing?
You did not mention if you have a stock valve train, ie torqued the rocker arm nuts down to 20 ft pounds, or have the adjustable poly-locks. It is possible that your valve are adjusted too tight in either case and being held open just enough to be a problem. Not saying this is the case as all your cylinder pressures seem consistent, but could be something to check.
If all this checks out, then I am onboard with a timing issue - whether cam or ignition.
Keep us posted and we will get it solved.