You're brave peeling that carpet up, I probably should have tried to save mine, but wasn't trying to fight the whole thing out, raining turds. Just cut it into sections, and into the trash it went. Also figured Id never get the smell all the way out.
No help here on the padding, etc. I'm going to end up coating my pans with monstaliner, or Ive also been looking at the replacement rubber floor, whatever they are called. Carpet and country just don't mix.
I think I would be pulling the dash, and door panels, then taking the power washer to the inside. Trying to scrub the nastiness out of the cracks, and wash it all away with a bottle of cleaner or something is not going to be pleasant, or get it all clean.
If you do wash it out, there should be a line of 1 1/2" body plugs along the underneath of the rockers on the inside facing the frame rails. You might pull one or two of those so it washes and drains them too. I don't know how crew cabs are laid out, but the mice had made nests in a foam/wire barrier at the bottoms of my extended cab section, which opens up into the rockers. They do/should have a normal drain at the back corner too though.
Dont know if it actually helped, but I grabbed a big box of baking soda and sprinkled it all over, wetted it all down, then let it sit before a rinse. Figured it would help neutralize odors, and any acids from the mouse pee, but I have no facts that it actually did anything. Truck smells nice now.
I probably went a little excessive, but I did not want to smell any damn mouse nasty after it was all said and done.