Hello fellow Honda-Techies, here's the problem:

Have had a repeated dead battery over the past two weeks:

1. Battery just over three years old, dead, overnight on charger, started up, dead next day.
2. Installed new battery, cleaned cables etc. Drove that day fine, next morning dead again.
3. Charged overnight again. Drove to NAPA dealer where the battery was bought; they tested the battery under load; battery, starter and alternator check out.
4. Hmm, parasitic drain? After charging overnight again installed battery disconnect on negative terminal to stop draining/ruining battery til the drain is diagnosed.
(Multimeter fuse was blown when I forgot to switch to VDC from mAmps so need new MMeter to try to track down drain)
5. Ran car to do errands (gotta buy food!) Started up fine, ran fine on local roads, on highway to 60mph to supermarket, turned car off. Started up fine, left store,
stopped at red light, check engine light comes on with a little shudder, light changes , accelerate, car hesitates, bucks a little bit as I try to accelerate, smooths out a bit but repeatedly
hesitates and bucks as I try to get it home about 7 miles. The check engine light stays on.
6. Turned off car in the driveway. After unloading groceries, attached my OBDII tool to see what the code was. When the key is turned to accessories to activate the scan tool, the check engine light came on
initially, then turned off. After scanning it says "No power train DTC's or Freeze Frame Data is presently stored in the vehicles computer". The I/M Monitor status ovals above the message showed:
Mis, green solid oval
Fue, green solid oval
CCM, green solid oval
CAT, red blinking oval
EVA, red blinking oval
O2S, red blinking oval
HTR, red blinking oval
7. Disconnected the battery to make sure it didn't go dead again and called it quits for the night.
8. Today, re-connected the battery and checked it again with the OBDII tool. Same results as the night before. Started up the car and took it on a jaunt around neighborhood roads for 15 minutes; got up to 40 mph at stretches. Car drove smoothly the entire time and the idle had settled down quickly to the usual 800 rpm.
9. Parked car in my driveway, turned it off. Checked the I/M Monitor ovals again with the OBDII tool.
All the previous greens stayed green.
The O2S and HTR ovals went green.
The CAT and EVA ovals remained blinking.
10. I left the battery connected. I had noticed the day before that the interior dome light did not go out after the usual brief time even though it was on the middle position (wow, maybe that's the problem!)
and turned the dome light switch to off.

So......
I'm thinking maybe the fuel trims are all off from the ECU being wiped repeatedly and I have to drive it a bit every day to re-train it?

The entire exhaust system was replaced from the A down pipe to the muffler including both O2 sensors just under a year ago and there's been no problems all year.

Am I dodging a bullet here? Is my thinking straight on this?

Thanks guys,
CaseyAtTheBat