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2006 Chevy Express 3500 4l80e swap into an 01 Chevy Express 3500

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Does a 2006 4l80e swap into an 01 with no issues and do the valve bodies inter change? Do I order a valve body for an 06 transmission or an 01?

I installed the 06 Transmission into the 01 and it worked well for a couple days. Now the fluid smells burnt and shifting is erratic or it defaults to limp mode. I disconnect the PCM to get it out of limp mode start it and it will start to shift somewhat but erratically through the gears and end up defaulting to limp mode rather quickly . No hard codes set the check engine light but 40to41 pending engine and transmission codes can be seen when I hook my scanner up and pull the pending codes.
 
There is a difference in the valve bodies between the 01 and 06. I believe 04 and up had the different valve body in them.
 
The only difference to my knowledge is the pressure control solenoid changed in 04 due to a supplier change, but both styles interchange with each other.
 
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