Just a guess: maybe the AEM ECU doesn't ignore the AFM while cranking to enrich the mixture like the OEM ECU does.
It can be tested easily, specially if one of you have open filter instead of the air-box.
Just remove the filter, put your finger to hold the AFM open a bit more that it should open on idle and ask a friend/brother/sister/mom/dad/dog to try and start the engine.
(as soon as it start running, remove your finger.)
If it start quicker than before, I'm right...
If I'm right, I might be able to build a small circuit that will replace your finger (for this use) and fake AFM reading while engine is cranking...
Disclaimer: I don't have and didn't had an AEM ECU, all the above is based on my knowledge on this engine, ECUs in general, knowledge in electronics and the data from this thread.