What you want is a mapping from pins out to pins in.

You need to make one of two assumptions here.

a) for one pin out there are few pins in

b) for one pin out there are an arbitrary number of pins in

I'd guess "a"

If so, I'd do this -

don't use line "0" as an input.

Now your eeprom data looks something like this

<list of 'in' pins for pin 1> 0x00
<list of 'in' pins for pin 2> 0x00
<list of 'in' pins for pin 3> 0x00
<list of 'in' pins for pin 4> 0x00
etc.

Now, if most cables are sparse on the output end too
(like an RS232 cable, fer instance)
I'd store it this way:

<output pin #> <list of 'in' pins for that out pin> 0x00

an output pin # of 0 terminates the list

so, for example, if it's wired
out             in
1       -       1
2,3     -       3
4       -       5,6
5       -       4
6       -       7,8

your data would be

1       1       0
2       3       0
3       3       0
4       5       6       0
5       4       0
6       7       8       0
0

You presumably will cycle through, turning one output pin on at a time.
otherwise you've no way of telling if it's shorted, cross wired, etc.
obviously you somehow have to float the other lines (weak pull ups).