Sadly there's nothing that makes the rearrangement part quicker, unless you're willing to code it out in GIMP or have Photoshop and use Actions. You'll have the most trouble with autotiles, since the format is completely different. 2k3 has a similar autotile setup to XP, so just squishing them down into the MV format is likely to result in tiling errors. It'll work out easier if you get that sorted before you upscale, though testing if it's working will be harder to do outside of MV. I have
a template for Pyxel Edit that would make that part easier, but if you aren't planning on redrawing anything buying the program wouldn't be worth it.
If you're wanting the default 2k3 tiles or another set that's freely available in MV format you might want to ask over in Resource Requests if anyone has already done it before you put in the work yourself. FYI, 2k3 had a lot of rip sets back in the day, those are not free to use and we do not support rips here.