2008 Dodge Dakota Cylinder 2 Misfire and Code while at idle?

3.7

A few weeks ago number 4 tossed a rocker onto the head(second time)(first time number 2). I have replaced the lifters, both banks. But since, I have had an issue with cylinder 2 misfire, at idle only. Will trip a code/ light. When it occurs, shortly after cold start up, when idling down from high idle. There seems to be a slight vibration/ starve for fuel condition. It lasts about 2 seconds, then code light. I have changed the plugs(6), and the coil on number 2 cylinder. Strange to have an issue with 2, when number 4 tossed the rocker.

Note. When changing out the lifters, the battery was disconnected for 3 to 4 hours(change out for new). When the work was completed, there was an erratic shift condition, and torque converter shudder. I took it to transmission shop for a reset/ re-learn.

I could change out the injector on Number 2, but I think I would be wasting my money. There were not any issues with number 2 before tear down.

I get the feeling that when I pulled the old battery out to do the work, then in with the new battery. The flash updates were wiped during reset. Or PCM has/is failed/failing.

Any Idea's. Thanks in advance.