Footwell fuse box...anyone have the layout of the fuses ?

[Red]

"betwen STOP and CIG fuses there is a unsued fuse, right? "
No, there is an empty and unused fuse socket. The factory does not waste a fuse in it.

"but my AE86 (with 4AGZE) has a fuse there"
I would guess that whoever installed your GZE engine, also did some custom work and used the spare fuse socket instead of adding a fuse to something else. Very nice and neat--but they also should have documented what it did.
Your best bet now is to remove the kick panel and see where the wire from that fuse socket has been connected to. Also check the fuse, sometimes just pulling it out and replacing it breaks the fuse internally and that's enough to cause a problem. Or their wiring may have just been tucked in, and come loose.