Tricky one... And a lot of "that said..." to follow.
What you have is what you have. 44.1kHz files aren't going to improve by being set to 88.2kHz. That said, some EQ's might push aliasing noise higher at higher rates. But that would work the same on export (rendering to 88.2kHz is going to put those plugs in a 88.2kHz mode). THAT said, many of such plugs already calculate at the first multiple just because of that. *THAT* said, can you hear a difference if you export in both sample rates? And if so, do you actually prefer the higher rate?
On to resolution / word length -- Same sort of thing. Ideally, you should've been in 24-bit from the start (avoids additional dithering noise, improved footroom for low-level signals, etc.). If you're in 16-bit at the moment, your DAW is likely calculating in (at least) 32 bit anyway - So again, modifying individual files isn't really going to help anything.
Side note on that one (which I couldn't get another engineer to understand a few days ago) -- If all your source files are 16-bit, you should *STILL* render in 24-bit. Those calculations are being done in a floating-point architecture and the benefits of the higher resolution are still going to be intact. You can't do anything about whatever dithering noise was on the source tracks, but you don't have to add more as long as you're in 24-bit.