If you go by your original idea and just wire the keys up to a matrix that is simple and then try to remap it, then you might end up with a matrix with keys on positions that the Arctosa might not support ... and you
will most probably get problems with rollover on common key combinations.
That is because a 2KRO matrix usually have lots of holes in them to avoid ghost keys - that have be be blocked.
Soldering-wise, it would be easier to do what lowpoly did and use a
Teensy 2.0 and wire your own matrix with diodes. That could also give you more features and n-key rollover. There are several firmware available for it. You could look at
Soarer's firmware: it doesn't require knowledge of C programming: you define the matrix and layout in a configuration file.
Yet another option would be to not modify the keyboard at all but to make a Teensy 2.0 into an adapter using
Hasu's firmware.