I don't have the game to look at.
Still you say BMP and while they may load then you might not be saving it back in the right format, or the game chops some stuff off/adds some stuff the baseline BMP does not.
Simple test. Open one of them up in your editor. Save it back without doing anything (or if you need to trick something then overwriting something with the same colour or changing it to another colour and overwriting it back) and then compare the files in a hex editor. If the changes are major then you probably have some fiddling with the settings on your editor to do, if they are minor then figure out what they mean (if anything) and replicate/correct accordingly.
Your basic Windows paint thing might not have that many options so you might need to grab a copy of GIMP, paint.net or something of that calibre. If you are lucky you might be able to fire your images through irfranview's batch mode.
"the TSC script files are different from the ones in the PC freeware version"
Can well believe it. You say unencrypted and that makes sense -- many PC games encrypt or protect their assets but devs assumed the console ones were less troubled, or did not want to pay the speed penalty. Even without that then the files might be simplified a bit, or have some more added to it if the DSiware version had things the PC version did not (or vice versa).
You might be able to figure out differences and create something to convert scripts, or use the output of a PC editor, but for the most part I treat any PC games or the same game on other platforms as sort of inspiration or ideas on what might be in there rather than something I can happily use here.
When you say replace levels have you tried copy and pasting a level from within the DSiware version (think delete level 3, copy paste level 4, rename to level 3's name)? This mainly to help eliminate whether it is a rebuilding error (or running error) rather than file format change between ports -- I am not familiar with all the various DSiware running methods but given how fiddly and annoying they are for plain DS games it makes sense to confirm first.
