I had never seen sandpaper used as a shim, especially this small and thin. So I threw it away
I hope you don’t work on anyone’s vehicle brakes….
From purchase date to the above event was about two years? Any problems other than the aforementioned seasonal truss rod adjustments? If not, then the bass is still salvageable.
I’ve used sandpaper as a shim material for at least as long as the time period you’ve never seen it used. I really don’t know how many bass necks I’ve shimmed, but I’d guess it to be over a dozen. All were successful as far as I can remember and sandpaper was the shim material in all. Necks don’t shift side to side with a sandpaper shim. Don’t discount the use use of sandpaper. For shim stock; it works well.
I cannot get the bass properly setup - no matter what/how I try.
Yes, you can. The proof it’s possible is the two years you played the bass before you took it apart.
Disassembling a properly functioning bass & having difficulty reassembling it back to previous playability isn’t the fault of the bass, it’s just an indication you haven’t been successful in getting it properly set up….yet.
I cannot get the intonation set. Every string is sharp to some degree no matter how far I move each saddle away from the nut.
Why are you trying to set the intonation when you don’t have the action set properly yet? Intonation is the last step after getting the neck relief & action exactly the way you want it, which you seem to indicate you haven’t achieved yet.
Speaking of neck relief; how do you have that set? Since you’ve had the neck off the bass (under NO tension) and you’ve been sanding &/or scraping on the back of the neck (generating heat & possibly back-bow pressure), there’s a better than average chance the relief needs attention.
You need to re-approach the whole set up process, be more methodical, and don’t give up until it’s back how it was the first two years you owned it.