For the charging message, I would check all the connections.....at both ends of the battery cables.
Also check the ground connections and the connections on the power distribution box.
You might also look into the PCM power relay.
A low voltage going to the sensors and/or PCM can cause all kinds of strange problems.
I would look into the voltage issue FIRST.
Lean codes are most often caused by a vaccum leak.
One thing might be the isolator bolts for the upper intake manifold.
Check the hoses for the fuel pressure regulator and the PCV valve.
I would also verify the crankcase breather line that goes from the rear valve cover (1999 and newer) to the big flex hose that connects to the throttle body.
Also look over this flex hose that connects between the throttle body and the air filter box.
Also, I would look at the IMRC actuators, on the 1999 and newer, they use 1 electric actuator to drive the IMRC shafts.
There are nylon clips that connect the shafts to the actuator, these clips are known for breaking and/or falling off, leaving the actuator shafts to flop about at random.
Transmission, I am sure that the shop is reading the codes that are present when the transmission light comes on.
One thing that is a common failure item is the Transmission Range Sensor, aka Neutral Safety switch.
I would also ask the shop to verify that you have proper fluid flow through the transmission cooler.....it can become clogged when a transmission fails, causing the transmission to overheat due to lack of cooling.