As painful as crawling over broken glass but I think I've managed to get Threading and Timers enabled (they were enabled in the old 68k library but weren't very pretty).
Code:
[AGA_CreateDevice]: devindex = 0
[SDL_VideoInit]: Initialize the video subsystem
[AGA_VideoInit]: START
[SDL_VideoInit]: Create a zero sized video surface of the appropriate format
[SDL_AllocFormat]: bpp=8 ncolors=256
[SDL_VideoInit]: Start the event loop
[SDL_StartEventLoop]: Clean out the event queue
[SDL_StartEventLoop]: No filter to start with, process most event types
[SDL_StartEventLoop]: It's not safe to call SDL_EventState() yet
[SDL_StartEventLoop]: Initialize event handlers
[SDL_StartEventLoop]: Create the lock and event thread
[SDL_StartEventThread]: START
[SDL_StartEventThread]: Create the lock and set ourselves active
[SDL_CreateMutex]: START
[SDL_CreateMutex]: Create the mutex semaphore, with initial value 1
[SDL_CreateMutex]: Creating sem
[SDL_CreateMutex]: Created sem
[SDL_CreateMutex]: InitSemaphore
[SDL_CreateMutex]: Inited Semaphore
[SDL_CreateMutex]: returning sem
[SDL_CreateMutex]: FINI
[SDL_VideoInit]: Calling SDL_CursorInit
[SDL_CursorInit]: SDL_CursorInit()
[SDL_CursorInit]: Create the default cursor
[SDL_SetCursor]: Called with valid Cursor
[SDL_SetCursor]: Draw the new mouse cursor
[SDL_SetCursor]: CURSOR_USINGSW
[SDL_TimerInit]: SDL_timer not already threaded, calling SDL_SYS_TimerInit()
[SDL_AddThread]: Threads already allocated(0) - max threads(0)
[SDL_AddThread]: Expanding the list of threads
[SDL_AddThread]: Threads allocated(1) - max threads(32)
[SDL_CreateThread]: Starting thread with args 102380c4...
[SDL_SYS_CreateThread]: Sending 102380c4 to the new thread...
[SDL_TimerInit]: SDL_timer started
SDL_SetVideoMode(width=320, height=240, bpp=8)
AGA_SetVideoMode(width=320, height=240, bpp=8)
AGA_SetVideoMode() SDL_HWSURFACE requested
AGA_SetVideoMode() SDL_HWPALETTE requested
AGA_SetVideoMode() SDL_DOUBLEBUF requested
AGA_SetVideoMode() SDL_FULLSCREEN requested
AGA_SetVideoMode() SDL_RESIZABLE NOT requested
Setting mode 320x240
[SDL_AllocFormat]: bpp=8 ncolors=256
SDL_SetVideoMode: surface depth of SDL_VideoSurface 8
AGA_SetColors()
AGA_SetColors() - firstcolor = 0
AGA_SetColors() - ncolors = 256
AGA_updatePalette()
AGA_updatePalette() - _paletteDirtyStart = 0
AGA_updatePalette() - _paletteDirtyEnd = 256
Requested mode: 320x240x8, obtained mode 320x240x8 (offset 0)
SDL_SetVideoMode() - Reset the mouse cursor and grab for new video mode
[SDL_SetCursor]: Called with NULL Cursor
[SDL_SetCursor]: Draw the new mouse cursor
[AGA_ShowWMCursor]: Showing Cursor
[SDL_ShowCursor]: SDL_ShowCursor(toggle = SDL_DISABLE)
[SDL_ShowCursor]: Hiding Cursor
[SDL_SetCursor]: Called with NULL Cursor
[SDL_SetCursor]: Erase window manager mouse (cursor not visible)
[SDL_SetCursor]: ShowWMCursor
[AGA_ShowWMCursor]: Hiding Cursor
[SDL_AllocFormat]: bpp=8 ncolors=256
[SDL_ConvertSurface]: 8 0 0
[SDL_AllocFormat]: bpp=8 ncolors=256
[SDL_SetPalette]: which=3, firstcolor=0, ncolors=256
[SetPalette_logical]: firstcolor=0, ncolors=256
[SetPalette_physical]: firstcolor=0, ncolors=256
AGA_SetColors()
AGA_SetColors() - firstcolor = 0
AGA_SetColors() - ncolors = 256
AGA_updatePalette()
AGA_updatePalette() - _paletteDirtyStart = 0
AGA_updatePalette() - _paletteDirtyEnd = 256
[SDL_ShowCursor]: SDL_ShowCursor(toggle = SDL_ENABLE)
[SDL_ShowCursor]: Hiding Cursor
[SDL_SetCursor]: Called with NULL Cursor
[SDL_SetCursor]: Draw the new mouse cursor
[AGA_ShowWMCursor]: Showing Cursor
[SDL_Quit]: Quitting all SubSystems
[SDL_SetTimer]: ms = 0
[SDL_DelThread]: Deleting thread, threads left(0) - max threads(32)
SDL_FreeCursor()
AGA_VideoQuit()
[AGA_DeleteDevice]: START