Dan,
Without the vac advance hooked up you will not get enough advance and the car will fall on its face during acceleration. Been a long time since i studied up on advance curves, but assuming a car can take 36 degrees total, 8 is initial (set with timing light), some is mechanical (and in your application should be in by 2500 to 3000 rpm. stock curve dist may not come in until 4000 or more). Perhaps 1/3 to 1/2 total advance is from teh vac advance unit. adjustable ones are available too. I would think you could hook up tht evac advance right to the intake port without a problem (i have done it...on a stock motor i never noticed muchif any difference). with only 10 in of vac you'll never get full advance.

total vac - a bit low (not for this motor, but in general). that is why the PCV is making things unhappy, it lets the total vac drop too low. not sure it this is related to the vac port on carb issue or not.

900 CFM is a bit of overkill for a 289. at 5000 rpm, at 80% volumetric efficiency you can only get 670 cfm into the engine (math available upon request). The carb/intake you have will be dog down low, but will scome into it's own up high in the rev band. assuming you have a proper cam for hat, and trans setup and rear gears...

when an intake valve opens and hte piston creates a vacuum, a column of air begins moving. it is still moving when you close the valve (momentum works on air too). for torque down low, use long small intake runners (see modern cars). your intake has your carbs a long way from the intake valves, so the column of moving air (with the fuel in it) has a ways to go, takes a while to get started, etc. I would suspect that there would be some throttle lag, particularly at low speed and off idle. This is probably why the accel pump change has worked. (you open throttle, but it takes a bit gor the engine to rev so the air/fuel it is sucking is still lean, by the time the good stuff gets there you are out of the throttle.)

I will be out of town this weeknd, but early next week i will get back to you...i will see if i have anything on tuning a tunnel ram (i still have my car mags rom the 80s...)

Low vac will somewhat confuse the carbs too...have to look up the fix for that. you could try using a vac canister (an air tight can hooked to intake port (brake vac line?) and then run the vac accessories off that.). Also, a vac pump is sold that runs off a belt like a water pump/alt, etc. not that this solution would help the advance issue, but if the brakes are run off that the vac left may be enough for pcv? Never used one of the aux vac pumps...perhaps they plumb into the intake too? see Summit or Jegs and then check the manufacturer's website.