Why does my transmission keep getting stuck in "limp-in" mode?

2003 Chrysler 300M
3.5L V6 engine
111304 miles

Hey everyone,

When I first start to drive my car its fine, but often when I decelerate (especially when decelerating fast or going up an incline) the engine will jerk and then remain in 2nd gear until I turn it off and back on again. I read online that this is called "limp-in" mode, and is a safety feature when something is going wrong. However when I drive the car in "autostick" mode, this doesn't happen nearly as often.

I took the car to my local dealership and they said they didn't know what the problem was, and they said they needed to take the transmission apart ("transmission overhaul") to find out what parts are needed. This will cost me $1,682.69 which I don't have, plus the cost of labor and whatever part needs to be replaced. Then below that quote they wrote "this does not include R&R complete transmission assembly fee - $3524", which I'm guessing means they are going to charge me another arm and leg to put it back together!

Do I really need a transmission overhaul? Is there some cheaper alternatives I can try to fix it? Here are the error codes along with the notes the technician wrote down:

P0562 - "Low battery"
P0952 - "Auto stick input circuit low"
P0731 - "Gear ratio error in 1st"
P1790 - "Fault immediately after shift"
P0841 - "LR pressure switch sense circuit"
P0871 - "Overdrive pressure switch sense circuit"
P1776 - "Solenoid switch valve located in LR position"

Any help would be much appreciated!