Stumble at idle when you first start up (2000 Chevy)

[jeffro788]

Hey guys, I am having a little issue with the truck not wanting to idle at first when you start it up and put it in gear. You have to pedal it to keep it running, but it will eventually straighten itself out and run perfect. It only happens right after you start it and put it in gear.
We have changed the fuel pump, pressure regulator, air filter, and checked the plugs. The idle air control has been checked and operates and all other sensors seem to check out. This happens whether it is hot or cold.
Just a little history on the motor (not stock at all), it is a LS1 (5.3L) lower end with 6.0L (317 stamped) heads, mild cam, whipple supercharger, bigger injecters, custom tune, headers, and 4" y-pipe with a Borla race muffler.
The transmission has a 3000 stall torque converter so I don't think the load is pulling it down.
Not sure if I am missing anything to check. It does run fine after a minute but not understanding what is going on.