360 stroked to 408. Running issues.

Jared mine did similar to yours when I first set it up with timing control it would sound like it was running on 6 cylinders and when I would increase throttle it would pop and back fire and what I did find was my timing wasn’t increasing with rpm and staying on 16 degrees. How to check it is go into Home Screen than tuning , than monitor look down the bottom of the screen while increasing rpm see if your timing changes increases . I found mine for some reason wasn’t moving off 16 initial timing reran wizard and it came good.