The seats themselves will be a direct bolt in however the 2000 passenger side seat will not have the airbag weight sensor in it that your 2006 does. (2000 had an/off switch for the airbag instead of a weight sensor).
The seat covers are not at all hard to remove, they simply velcro on so you can replace the drivers side seat completely and then just swap the good cover from the 2000 seat onto your current passengers side 2006 seat. Unless the foam itself is also trashed. The foam is attached with hog rings so that can also be swapped but will require alot more work.
I do not know if it's possible to swap the weight sensor itself since its somewhat integrated into the bottom of the seat.
As far as I know the connections for the seat belt retractor and track position sensor on the drivers side are the same connection between 2000 and 2006.
You can also ditch the 60/40 split and get new seat covers for your current seats. I recently did this to my 2009
Seat swaps being out of the question on a regular cab I gotta do what I can to make the stock seats more comfortable... Step one - KILL THE 60/40 SPLIT!!!! To my suprise removing the side seat on my 2009 is actually much easier than on videos I've seen of older trucks. There is no solid pan...
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