Greetings!
Well… Let’s take a look at this… You still have the original carpet & padding, but have bolts sticking up through it right? While I can’t picture the uneven floor, I use those bolts to secure my cabinets, bed, and other furniture. I keep the original carpet & padding intact, and just use throw rugs over the top of it.
If you have bolts sticking up where you don’t want them, they can be removed or cut off, just make sure you aren’t left with unplugged holes going to the outside.
I also try to keep the walls & ceiling intact if they aren’t trashed beyond salvation.
For my cabinets, I start by building a L out of plywood that will serve for the base and back of my cabinets, and secure them to the seat mounting points. Now I have plywood to securely attach my cabinets to without drilling any new holes into the van or damaging the floor/walls/ceiling in any way.
I can elaborate more if needed…
Of the two choices you listed, I too would choose the bed rug, if I couldn’t make the original floor work… That being said, by your description, you may still have to deal with solving the uneven floor & bolts problems.
Good Luck & keep us posted!
Cheers!