More importantly, I've solved the crash issue this was due to CGDoom attempting to return direct Flash addresses without allocating RAM when accessing lumps that are stored as a single fragment in Flash. (Only the load/save feature is still disabled.) I've made a few changes to GUI: I added the brightness/gamma setting on the FRAC key, fixed menus that didn't work, added the space/return key for confirm screens (EXE/log on the current keymap), and added a main screen setting to warp to a level when starting the game.
Great news! All the levels of the shareware Doom now load, and all the levels of Ultimate Doom except level 6 load as well.