Not the exact problem but something somewhat similar.
When I start mine from a cold condition it will go through a short time period where it has a lot of misfire and pop back. Almost a pinging type noise. It almost sounds like an intake valve not closing but I do not think that is the cause. I have replaced the spark plugs to no effect (and please don't try to push the Ford plugs on me) and redone all of the split second wiring, also to no effect.
It is not consistent but always occurs during the warm-up. If I immediately drive after starting I will not notice it but it is most apparent at idle and off-idle. I believe it to be sensor or the Paxton add-on control unit related (could be a huge spark retard during the open loop idle/low speed operation has the spark so late as to cause backfires).
Note I had well over 1000 miles on it before having this condition.
Are you using the split second unit?
If so that would be one point of commonality with me.