Will NOT run right!!!!!!!!!

Sorry, been out of pocket. It is a hydraulic system, xe250 - 250/260 - 206/212 - .425/.444, basic holley vac secondary 600, eddy performer intake, headers,duels, flowmasters. Daily driver car and it does great when you first start it (cold) but put about ten miles on it when it's warm and it starts missing.
Fuel pump is new from Napa, mechanical. Fuel bowls are side hung but, it misses and dies at a stoplight just sitting there, no turns. Bowls are set good.
Plugs gapped at .035
I mostly turn right, but it doesn't seem to matter. If I'm out on the road/highway no problem, but when I slow down or come to a stop, you have to be ready. Sometimes I can kick it into nuetral and it won't happen, but put it in gear and it will try to die. If I turn the Idle way up,800 rpm in gear, it still happens so I don't understand the nuetral thing.
In the end, it only happens when it warms up, not when its cold. Wondering if it could still be a vac. leak somewhere around the manifold or carb base? Oh, and it happens evertime I drive it.
This car is an original 27,000 mile survivor. Pulled the six and put in the 318. Changed the carpet, brakes, new suspension, exaust annnnd done. Great little daily driver, just wish I could figure this. Haven't changed the ballast yet, might as well.