initial timing set at 12 total 39 at 3200 rpm. 6-10 vacuum advance.
idle set to 650 in drive making 13-14 in Hg and 17 in Hg in park

I have tried two carbs. a autolite 4100 and the holley. my first thought was the accelerator shot but I wanted to make sure everything else was ok before messing with the carb.

 

If you have a slight vacuum leak, then that would explain why you might have a lean mixture causing your hesitation. 6 deg? should pick it up to at least 10 deg.If you're running the stock spacer, they tend to leakbetween the manifoldand the carb, if you're running an after market carb and manifold. I ended up pulling my stock spacer andwent to a 1" phenolic spacer, and completely eliminated any vacuum issues. btw, stock vacuum is 19-22, with a mild cam 15-19. 13 seems a touch on the low side.

 

I have a 1 in phenolic spacer. I sprayed carb cleaner around the base of the carb and all vacuum trees and conections. there is not any change in rpm or running. could bad ignition cause poor vacuum? or could a internal leak, such as where the intake meets the heads, cause poor vacuum at idle?

 

yes to all those, pull the spacer off and try it, if it goes away you need some carb tuning. and again read your plugs.......I had a similar problem after I installed a 1/2" spacer on my 408.

 

okay, stupid question. should I be reading my vacuum in drive (under load) or in park/nutral (no load) because if it is in park I have like 16-18 in but in drive I have 12-15 in. also should I set my idle speed in drive or not and what rpm is best for that cam? thanks.

 

adjusting pump shot is nothing, just mess with it till it is a strong, straight shotat first touch with the bigger nozzle. do that to get your car running better.

your car likes the cold better because when warming up or cold, it can accept the advanced timing you have. Get it timed right.

my car was having these exact problems/issues and worked much better when i timed it and adjusted the shot with a bigger nozzle.

 

What makes you think the timing is too advanced? 12 at idle and 39 total seems about ballpark for a mild 289.