KC, I don't know if you've been running this setup successfully and it "just" developed a miss, or whether you've just fired it up for the 1st time, but I had issues with AEM's 2820 box when I tried it on the Ferrari, similar to what you're describing, although my miss was around 5000 to 5500.
It was a noticeable "stumble" during acceleration after the engine was warm. Wouldn't do it when cold, however. I was running the 12 cylinder on waste spark and only using 3 channels per side on the 2820. Had it wired correctly, and tried the coils both in parallel and in series with no change. Tried a 2nd 2820 box and it did the same thing, then I finally eliminated the box altogether and went back to an inductive setup, and the miss was gone.
AEM has had issues with these Twin Fires since they came out years ago, and they've finally stopped making them now, which was probably the best thing they could do to "improve" the product.
In your case, I would pull the AEM out of the system and try a straight inductive setup (just ECU, ignitors and coils) and see how it works. If you have only 4 ignition channels and you must run waste spark, I'd run 2 x 4 channel ignitors to get a "4 in and 8 out" setup, and parallel the ECU triggers into the ignitors so that each coil gets an individual, dedicated ignitor output.
You'll get a hotter spark this way and the system will be happier. Alternatively you can try paralleling the coils, but this typically confuses the ignitors, or you can try putting the coils in series, but this splits the charging voltage to each coil, and I don't believe they develop full output.