Can't keep 408 running
 

I fired up the 408 today and can't keep it running. I am using a 6.0 tune right now with the cylinder volume changed to reflect the new motor and the VE scaled up 3% like it was recommended to thunder550 when he did his 408. My cam is a 244/248 .612/.615 on a 112lsa

I drilled another small hole in the throttle body to get a bit more idle airflow and it didn't seem to help.

One hole in the TB is plenty enough; it needs increased airflow in the idle and startup tables. Assuming you increased the entire VE table (including lower rpms), this would usually worsen the idle and startup. Can you keep it running with your foot on the gas and are you datalogging?

Try this;
I would raise the idle speed for both Park and Drive to at least 900 rpms. Then reduce the values in the lower VE table (0-1200 rpms) in 5% increments. You also need to increase the Desired Airflow in both Park and Gear. For startup; you can increase the values in Startup RPM Offset (adds rpm to startup based on coolant temp), increase the values in both the Startup Airflow Correction and Startup Airflow Correction tables. Depending on the timing, I would look at increasing spark in both Park and Drive. Every combination takes a different amount of adjusting, so you will have take your time between datalogging and tuning.