I took it down to Ford and paid them $50 to do an electrical diagnostic check and also in the hope that the mechanic had messed with a ground or something when pulling the wire loom loose to replace one of the fuel filters.
As suspected, the alternator has intermittent output which they blame on one of the starting batteries being bad. That could be the case, but geez they're only a year old. At least there's some warranty left on those. Anyhow, sometimes you just don't know what to believe but here's what they told me after I mentioned replacing the failing unit with a high-output one:
-Stock is indeed 110A but Ford doesn't recommend putting in a bigger one (I assume higher output not just the case size) because it will short out the instrument cluster
-And because it's PCM controlled the computer will never let it get full output
-$504 for the same alternator new
-don't go aftermarket because the system is synergistic and will only play nice with a motorcraft.
I believe I'll be placing a call to DCpower here shortly