Missing and running rich
 

My engine ran flawless up untill the last time I ran it.
The weekend before it ran flawless.
I left a panel light switch on by accident and ran the batteries stone dead. Batteries were DEAD for a week.
Was at launch ramp so I jumped it to my truck for 30 minutes ( boat on trailer next to truck - both out of water)
Boat fired up but for some reason the alternator wasn't charging and the batteries were only at 11 volts.
The boat ran like crap. I have Holley HP EFI. I figured it was because of the 11 volts.
Had the alternator tested and it was OK.
I checked all of the wiring and everything was OK. And on the hose it runs and is charging. ???
But it is still missing - you can hear it dropping cylinders and then firing. It is also getting the back of the boat black in just minutes.
I have an MSD box.
I also plan on going to CNP ignition so I don't want to buy another MSD part.
Is it possible the low voltage messed up the EFI program???
I could always reload the original program but don't want to lose the learned changes.

When you said 'learned changes' are you saying that it was on 'auto tune' during that mishap ?

Yes it is still on auto tune. I did a blending a few weeks before the incident.
Are you telling me I lost that?

If you have a plug fouled the O2 will read lean. If you are running closed loop the engine will go way rich because it can't compensate for the extra O2 from the fouled plug.

If you transferred the learn table to the map a few weeks ago you could go in and zero the learn table and that would put you back to where you were then.

This. ^^^
Why I believe Auto Tune should be turned off when all is okay. I know some people that leave auto tune onall the time. would make me nervous. 1 of them is on a sled where the chances of killing an 02 at any time us very real. Doh !