Well, after doing some more research and experimenting, I seem to have the graphics opening properly in Tile Molester.
Once I get a couple more things figured out, I'll show how to get it working.
EDIT: In general, here's how it seems to work:
The typical game has 8 graphics ROMs, labeled 13-20. The first half of the graphic data is formed from the odd-labeled ROMs, the second half is formed from the even-labeled ROMs.
Each of those halves are composed of chunks 1,048,576-bytes long, which alternate between the even and odd words of the ROMs composing them. Meaning that the first 1,048,576 bytes of graphics data is composed of the first 524,288 even words of the associated ROMs, the second 1,048,576 bytes is composed of the first 524,288 odd words of the associated ROMs, the third 1,048,576 bytes is composed of the second 524,288 even words of the associated ROMs... etc.
Within each of those chunks, words from two of the associated base ROMs are interleaved for each 8x8 subtile (64 bytes). The ROMs read from alternate between each subtile. Meaning the first subtile is comprised of interleaved words form the first two of the four associate ROMs, the next tile is comprised of interleaved words from the second two of the four associate ROMs. So, for example, the very first subtile would be comprised of alternating words from ROMs 13 and 15, the second would comprised of alternating words from ROMs 17 and 19, the third would switch back to alternating words from ROMs 13 and 15... etc.
So to get the graphics loading in Tile Molester you need to follow these 5 easy (?) steps:
1. Split each base ROM into its even and odd words.
2. Interleave these on a word basis into eight files: The 13-15 evens, the 13-15 odds, the 17-19 evens, the 17-19 odds, the 14-16 evens, the 14-16 odds, the 18-20 evens, and the 18-20 odds.
3. Interleave each half's evens together and each half's odds together, both on a 64-byte basis. You should now have four files: the 13-15-17-19 evens, the 13-15-17-19 odds, the 14-16-18-20 evens, and the 14-16-18-20 odds.
4. Interleave each half's odds and evens with each other on a 1,048,576-byte basis: You should now have two files, the 13-15-17-19 and the 14-16-19-20.
5. Append the latter to the former.
The file should now open in Tile Molester with the following settings: 4bpp planar codec, row-interleaved.
NOTE that this will only work for the 16x16 tiles. There are also 8x8 and 32x32 tiles stored in the same data, but working with those will likely require another method.
EDIT: Corrected a mistake: The graphics alternate between even and odd words on a megabyte (1,048,576 bytes) basis, not 8192-byte. The latter number is the amount of tiles in a megabyte of data, I confused it for the amount of bytes. Sorry about that.
EDIT AGAIN: Somehow I overlooked the switching between ROMs from tile to tile... Man, with how clumsy I am about this stuff it's a miracle I got it working at all. But now that I've run through everything again it SHOULD work as written. *Crosses fingers*