I don't have my DSTT set up any longer, but here are the files I had:
/TTMENU.DAT
/TTMenu.nds
/YSMenu.nds
/TTMENU/
/TTMENU/skin/
/TTMENU/skin/default/
/TTMENU/skin/default/... (skin .ini and .bmp files)
/TTMENU/infolib.dat
/TTMENU/language.ini
/TTMENU/reset.mse
/TTMENU/savlib.dat
/TTMENU/system.ank
/TTMENU/system.fon
/TTMENU/system.l2u
/TTMENU/system.u2l
/TTMENU/ttreset.dat
/TTMENU/ttsystem.ini
/TTMENU/USRCHEAT.DAT
/YSMENU/
/YSMENU/YSMenu.ini
/YSMENU/ttdldi.dat
/YSMENU/ttpatch.dat
/YSMENU/YSMenu1.bmp
/YSMENU/YSMenu2.bmp
/games/
/games/... (game .nds and .sav files)
I would suggest making a backup, wiping your microSD card clean, then re-installing the official v1.15 firmware (TTMENU.DAT and TTMENU folder). Create a "games" folder and put your .nds and .sav files there (leave plenty of free room for save files). Then start it up and confirm that the official menu works properly.
Once confirmed, rename "TTMENU.DAT" to "TTMenu.nds".
Get the latest YSMenu (YSMenu0809132222) if you don't have it. Place YSMenu.nds at the root of your microSD card. Make a COPY of YSMenu.nds named TTMENU.DAT (that should be the one run by default). Make a "YSMenu" folder on the root of your microSD card. Run "ttextract.exe" on the official TTMENU.DAT file to get ttdldi.dat and ttpatch.dat. Place those in the YSMenu folder. Edit YSMenu.ini and place it in the YSMenu folder. Place YSMenu1.bmp and YSMenu2.bmp in your YSMenu folder.
At this point, your setup should look pretty much like mine above.
-Bri