I had a similar experience this summer. I got a new Roush 427SRX, came with the same distributor you have. This was a warranty replacement for my previous Roush 402R (used a quart of
oil every 300 miles and could not be fixed). The previous motor came with a different distributor that ran through a 6AL box, no problems. When we installed the new motor with the different distributor it came with (same as yours with both mechanical and vacuum advance) we could NOT get proper mechanical timing with the vacuum disconnected and plugged. I talked with Roush, talked with MSD, etc. We got it to run, but instead of the nominal 16 degree mechanical advance (16 initial, total was supposed to be 32) we got 16 initial and over 40 total. It was worse with the vacuum connected. We fooled around with it and set the mechanical advance at 10 initial, which gave 34 total, and it ran OK, but that's still too much advance, and the idle wasn't very good (too retarded). Ultimately we simply removed the 6AL box and ran the coil directly from the distributor.
Voila! 17 and 31 degrees of advance, problem solved. The distributor has its own circuits so it doesn't need the 6AL to run, and the two don't play well together. MSD instructions for the distributor include a wiring diagram for the 6AL (available on line through the MSD site), and we wired it that way, but it screwed up the timing. The 6AL doesn't do anything above 3000 RPM anyway, so it's not needed.
You can do the same - I bet it solves your problem.
grybrd123