For whdload games JIT is useless, it causes more problems than the benefits it offers.
For stuff like Workbench however (the Amiga's OS) and non-whdload games that need the horse power (mostly 3D stuff) JIT can come in very handy.
I personally never use JIT in WinUAEX as I only use WinUAEX to play old school games. Even AGA WHDLoad games struggle so I doubt I'll want to play any complex 3D games (even if it will run them).
I'll sort you out the whdload.hdf file (and game file) as soon as possible, might end up being next week some time though as I'm pretty tied up from now until then.
I'm not a big fan of the default keymappings. I have a USB mouse and keyboard so I don't need the mouse being mapped to the analog stick. I've also completely changed the keymaps so that both the DPad and left analog stick are registered as a joystick (only the dpad is by default).
A good option for a few configs would be:
Joystick - standard 2 button
CD32 Pad - with all 6 buttons mapped correctly
Pinball - the amiga had quite a few decent pinball games, so mapping F1 to start, and the two shift keys to the triggers would be a good idea (or something similar).
On a normal Amiga the red button on the CD32 pad would work as the standard button on a joystick, although in WinUAE/WinUAEX the two things are separate (i.e. if it's set to Red, it will not work in games which do not have CD32 pad support).
Yeah that was the impression that I got about JIT when reading about it in regards to whdload and useage. I figured most people would be using winuaex for games. Worst case scenario I release a 2nd (no movie previews) edition.
On configurations. Not very many people are gonna have mouses. Even I only have one cable which I usually plug a keyboard into. But maybe if I go the preset configs route it can take the mouse mappings into consideration. The biggest fluke with that is, even without a mouse some games/titles want the user to press the mouse button.

I'll have to look into that red button issue, although I'm not sure if there is any point other than accuracy. Since the user really should be assigning the joystick buttons in non CD32 titles anyways.

Here are the standard emulator definitions for winuaex.. (32 entries)
CODE
{ "Joy1 Up", JOY1_UP },
{ "Joy1 Down", JOY1_DOWN },
{ "Joy1 Left", JOY1_LEFT },
{ "Joy1 Right", JOY1_RIGHT },
{ "Joy1/Mouse1 Btn1", JOY1_1 },
{ "Joy1/Mouse1 Btn2", JOY1_2 },
{ "Joy1/Mouse1 Btn3", JOY1_3 },
{ "Joy1 CD32 Play", JOY1_CD32_PLAY },
{ "Joy1 CD32 Rewind", JOY1_CD32_RWD },
{ "Joy1 CD32 Fast Forward", JOY1_CD32_FFW },
{ "Joy1 CD32 Green", JOY1_CD32_GREEN },
{ "Joy1 CD32 Yellow", JOY1_CD32_YELLOW },
{ "Joy1 CD32 Red", JOY1_CD32_RED },
{ "Joy1 CD32 Blue", JOY1_CD32_BLUE },
{ "Joy2 Up", JOY2_UP },
{ "Joy2 Down", JOY2_DOWN },
{ "Joy2 Left", JOY2_LEFT },
{ "Joy2 Right", JOY2_RIGHT },
{ "Joy2/Mouse2 Btn1", JOY2_1 },
{ "Joy2/Mouse2 Btn2", JOY2_2 },
{ "Joy2/Mouse2 Btn3", JOY2_3 },
{ "Joy2 CD32 Play", JOY2_CD32_PLAY },
{ "Joy2 CD32 Rewind", JOY2_CD32_RWD },
{ "Joy2 CD32 Fast Forward", JOY2_CD32_FFW },
{ "Joy2 CD32 Green", JOY2_CD32_GREEN },
{ "Joy2 CD32 Yellow", JOY2_CD32_YELLOW },
{ "Joy2 CD32 Red", JOY2_CD32_RED },
{ "Joy2 CD32 Blue", JOY2_CD32_BLUE },
{ "Space", 0x80000000 | VK_SPACE },
{ "Enter", 0x80000000 | VK_RETURN },
{ "0", 0x80000000 | '0' },
{ "1", 0x80000000 | '1' },
Mouse 1 button 1 = Y
Mouse 1 button 2 = black
Mouse 1 button 3 = white
Dpad is mapped to Joy 2
Joy2/Mouse 2 button 1 = A
Joy2/Mouse 2 button 2 = B
Joy2/Mouse 2 button 3 = X
Joy2 green (CD32) = A
Joy2 yellow (CD32) = Y
Joy2 red (CD32) = B
Joy2 blue (CD32) = X
Now I always figured that Joy1 on a CD32 would be the default stick mapped as player 1. Is that not the case?
I typically unmap joystick 2 buttons 2-3 (do any games uses 2?) and mouse 1 button 3.
Then..
Joy 2 up = B (since alot of platform style games use up for jump).
Mouse 1 button 2 = Y.
Space = white (since alot of games seem to use it).
F1 = Start (since some games use this to start).
That generic setup seems to work pretty well for me.
I really have to wonder the point of having mappings for joystick 1 (two player games?).
Also the last three entries (enter, 0, and 1) are at least questionable.
Anyways I need to come up with a default setting that is as generic as possible. Let me know what you think of my above settings and any thoughts on that. I suppose mapping the mouse to the right analog stick and the dpad to the left analog stick might come handy as a setting.
All the rest could be set-up as pre-set configurations (as you suggested).
Lemme know what you think. Oh one other possibility (didn't see many games use it though) is mapping the dpad to the arrow keys. It was useful for atarixlbox. But so far I have not run into many Amiga titles that seem to rely much on the arrow keys.