Very interesting...

that the secondaries are being forced, or drawn, to one side of their bore. Is the actuating arm at 90 degrees to the throttle lever? You seem pretty darn handy, though your wife seems to have a different opinion(typical), so maybe you could make another actuating rod out of coat hanger wire and monkey with the angle of attack. As to the vacuum at idle, shop manual says 17 for big blocks, 18 for 289. Is you engine warmed over? Mine has a very mild cam upgrade, 202 degrees both int/exh @ .050, stock is 192/199, and dual exhaust, yet I can only get 15 inches at idle. But my engine is old and rarely run so gummed-up rings may be at fault. In your case, I'd say the rings aren't seated yet so I wouldn't worry about a "low" vacuum reading of 15, yet. As you noticed, timing has a big effect on vacuum, as does mixture. If you can remove the exhaust pipes from the manifolds, as opposed to trying to separate mufflers and tail pipes, you can run the engine at idle (no load) without too much noise. You can pretty much ignore the factory timing recommendation since fuel is SOOO much different nowadays. In fact, the factory manual I have actually mentions advancing the timing around 5 degrees for better performance.