As a ROM hacker, I've had to go and "customize" my ROM quite often to get it to do what I want. As a result, I've found many useful tidbits of information, and I've decided to compile them all into one useful thread. Some of these come from other people; if I forgot to credit you, please tell me!
The reason is because when Tile Molester opens a ROM, it saves some settings, such as saved palettes, to an external file. This external file uses a Document Type Definition file called tmres.dtd. It saves properly; however, upon opening it, it needs the file and cannot find it in the folder, so it simply doesn't open the ROM right. This is simply because the Tile Molester hacker forgot to include that file in the download.
To fix this, open a Tile Molester download (non-Alternate), navigate to the 'resources' folder, and copy and paste the tmres.dtd from that folder into your Tile Molester Alternate's 'resources' folder.
They also have separate font width tables. These are what determine how wide each letter in pixels is. The tables are at 0x1FB100 for other, 0x207300 for black, 0x217618 for blue, and 0x227930 for red.
The 32-bit value at 0x78C1C controls how many frames the game goes through before it resets itself. There are 59.737 frames in one second. Determine how long you want the title screen to stay before resetting using that formula. (Thanks to knizz for telling me!)
To patch, navigate to address 0x110F54 and replace "00 28 0F D0" with "00 1C 0F E0". All this does is disable the check for flashback-worthy events, and simply loads the save like R/S/E.
Well, that's what I have. If you have anything to add, just reply and I'll be glad to add it in.
I hope this thread is a handy resource for anyone that needs it.