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Ensure that the mod does not have any map number greater than 94. You can use Booster's Lab to delete unneeded maps and it will automatically rewrite <TRAs for you. If you haven't broken the limit then ignore this step.
Starting Map and Events
You need to make sure that the starting events, maps, positions, stats, etc are as default (check this with cave editor). If they aren't then make them so and modify the default starting event to take you to to mod's original starting event, map, and position with a <TRA. If the default starting event is already used for something in the mod then something like this should suffice:
Where you need to fill in w, x, y, and z with your choice of map, event, etc.
And in the map and event you asked for use <FL+4620 at the very beginning before anything else. Feel free to substitute this with your own choice of flag number (with the <FLJ changed to match).
Rename all .pbm files to .bmp with a mass renamer. Look for 24-bit .bmp files (you can sort files by "bit depth" in windows vista and up) and convert them to 8-bit .bmp files using your program of choice. If you are not sure try using the Image > Mode > Indexed option in gimp.
Rename all .bmp files to .pbm with a mass renamer.
Rename your mod's data folder to "data2". Extract the contents of data.csz from an unmodified copy of Cave Story for PSP. Copy this new data folder to your mod folder. Move the contents of "data2" to "data", overwriting files as you go. Delete the now empty "data2" folder.
Use "export stage.tbl" under "File". Now look for a file called "csmap.bin". Use a hex editor like XVI32 to truncate "csmap.bin" to the same length as "maps.dat". Rename "csmap.bin" to "maps.dat" and delete "stage.tbl".
The lounge Bug
Yes that lowercase "l" in the title was intentional. Search your new maps.dat file with a hex editor for the string "lounge" in that exact case. Rename it to "Lounge". This problem doesn't crop up on windows, but on more case sensitive systems such as the PSP the map won't load and the game will crash.
Copy maps.dat to the same folder as an unaltered CS psp eboot and run this tool (which should also be in the same folder) to inject it into the eboot:
If you wish to see the output of the tool (because windows is too fast to terminate dos applications) then create and run a .bat file with the following contents:
Remove these extra files afterwards.
Custom Orgs and Credit Images
Resource hacker can extract these from the windows exe for you.
Pack the mod's data folder using CSZ Tools, test the mod, and use PSP Brew to add any icons or background pics.
Keep in mind this doesn't account for custom weapon edits (a little more complicated to explain since you need to find it, extract it, and insert it manually with a hex editor) or ASM hacks (for obvious reasons).
If you need any help with all this then let me know and I will assist you however I can, or I could convert it for you if you want.
But it's cool. The recent versions of Booster's Lab kinda made the process a bit more straightforward (no more TRA micro-management or manual extraction of mapdata by eye with a hex editor), so consider this the definitive guide as of writing.