Hey guys. I noticed that there's no info on the ff7input.cfg file's format, so I did some digging. This is definitely not my area of expertise however, so this is only preliminary.
Offsets - Keyboard
00 - Gamepad detection(???)
01 - Camera
05 - Target
09 - Page Up
0D - Page Down
11 - Menu
15 - OK
19 - Cancel
1D - Switch
21 - Assist
2D - Start
31 - Up
35 - Right
39 - Down
3D - Left
Offsets - Gamepad
61 - ???
65 - Camera
69 - Target
6D - Page Up
71 - Page Down
75 - Menu
79 - OK
7D - Cancel
81 - Switch
85 - Assist
91 - Start
95 - Up (E3)
9D - Down (E4)
99 - Right (E6)
A1 - Left (E5)
There's only a few offsets (aside from the ones I noted here) that I don't know the function for. There are some that have the same values that are at the gamepad's direction input offsets too.
EDIT: I went ahead and removed all the gamepad assignments so that JoyToKey can be used. Here's my modified ff7input.cfg (and named after a similar modification that's sadly seemed to have disappeared) and also my JoyToKey config files.
http://www.mediafire.com/download/46dl9z3llwum5b6/NOJOY_J2Kcfg.7z