I think that putting the Fire buttons on rows 0 or 5 of J,K and L columns will give us three fire buttons for each joystick port. The three buttons can be read with only one IN (0xB6h) instruction.
(I believe that is why the designer of the Enterprise put the lecture of the joysticks in rows, theoretically you can connect upto six(with only one fire button), but then you can save processor time reading three joysticks at the same time.)
The mouse can share the right button(row 0, L column) with third Fire button of Joy 1 for backwards compatibility with the Boxsoft interface. Or you can leave pin 5 of the DB9 not connected and forget third Fire buttons. I think it is enough with two Fire buttons.
But we need imperatively the Left mouse button at row 0, K column be at the same time the second Fire button on Joy1. I think it doesn't matter for normal use.
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The pinout of the DB9 joystick connectors can be as this:
1 UP
2 Down
3 Left
4 Right
5 Fire 3 Not standard, only Kempston joysticks. Normally not connected, or used for mouse-pad signals on Atari-Amiga connectors.
6 Fire 1
7 +5v
8 Ground
9 Fire 2 Not widely used for fire. Yes in Kempston. On Amiga connector can act as second fire or for mouse-pad signals like on Atari connectors.