Thanks to all the posts on how to do this. For anyone who is still converting but finds the few steps in MS-DOS a pain (opening the prompt, navigating, etc.) I wrote two quick bat files. For my own purposes I made a folder called chdtrans on my c: drive and do all of the conversion there, then simply erase the unneeded files after moving the rest. You'll need IsoBuster (free version works fine for this method and is linked elsewhere in this thread), gdrom2rom_gui.exe (google it from snk-neofighters.com), bin2iso.exe and chdman.exe (also available earlier in these posts. Place these executables in the folder you'll use (chdtrans for me) and then shortcuts for notepad, isobuster, and the two bat files I've attached (Step1.bat and rename iso to track03.bin.bat). Then follow the following steps:
1. Place whatever chd you're using (ex. slashout - gds-0004.chd) into the transfer folder.
2. Double-click the Step1.bat. Step1 renames the chd to 1.chd, runs the chdman bin extraction, deletes the 1.toc file, runs the bin2iso.exe command, then opens up notepad.
3. Replace the last entry "AUDIO" with the text "MODE1/2352" as stated in previous entries and save.
4. Drag the cue file onto your IsoBuster shortcut to open the image.
5. Right click the last track, choose Extract -> RAW DATA (bin iso etc); this will make a Track ##.iso file. Make sure to close the IsoBuster window now.
6. Double Click the rename...bat file to rename the iso to track03.bin.
7. Double click the gdrom2rom_gui.exe and type the number in for your conversion.
8. Move your two new files into your Naomi images folder and delete the remaining unneded files (labeled 1.*) If needed, the rename bat could also do this with an added line: del 1.*
This is the same process, but the bat files do save some time and hassle.