Several questions;
1) Are you running Speed density or Alpha N mode?
2) Doest it take a while to crank then start?
Go into your C Comp software and take a look at your Idle Speed vs coolant temp calibration and make sure your idle speed is set high enough.
Take a look at your Start IAC vs Coolant temp map. You may have to add some more IAC during start to get it to crank over better.
If those look good you may want to look at your timing trim and IAC trims.
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