Backfiring and hesitation after driving through puddle

Hello,

When driving through a parking lot on 6/24 during a thunderstorm, I was forced to creep through a large deep puddle. The engine did not stutter or stall, but beginning the following evening the car would randomly start backfiring through the exhaust at low RPM's, most commonly under decel when coming to a stop, accel from a stop, or at idle. On 6/30 I noticed my check gauges indicator was dimly flickering, but all my dash gauges indicated no problem, however I have not noticed it since then. On 7/2 I noticed on a one hour round trip that it would give really brief hesitation at cruise, be less responsive on the throttle, and new light bucking under 2000RPM. I installed new ignition wires and spark plugs maybe a month ago. Before the water puddle but after the new plugs/wires, I noticed I had a low voltage problem above 4500RPM, it's possible the charging system needs to be checked although I don't know if it's related specifically to the post-puddle symptoms.

I've replaced the PCV, cleaned the MAF sensor, logged all misfire activity during driving (I have an aftermarket cam so some misfires are to be expected, but no cylinders had an excessive amount or were climbing excessively quickly, I've seen them do so years before with a broken valve spring), performed a cylinder balance test (no problem detected) and had a fuel pressure diagnosis (injector cleaning performed).

I'd rather try to diagnose the problem than randomly throw new parts at it. Can you suggest a series of steps to isolate the problem(s)?

Thanks!

Jim