Sounds like you've got a good handle on it. Getting the carpet and padding out and getting it clean and DRY is key. Don't be afraid to really soak any muddy carpet with a garden hose, and use the shopvac liberally.
On Liberty's specifically, there's a power center of sorts under the driver's rear seat IIRC. If it got wet/muddy, make sure you clean the crap out of that sucker, and dry it really well. Corrosion at that area has caused vehicle fires... It does not like being wet, even occasionally.
Then realize that your Jeep isn't magic... It's made of the same components that are in a Ram, or a Chrysler 300. If you continue to flog it at every mudhole you see, you'll have LOTS of issues pretty quickly. (Do I sound like your mother/father?)
Oh, and make sure the door drains aren't filled with crud too, so they don't rot out from the inside.
At least it wasn't salt water, and you really weren't in that deep...
C
