I have the 93 Protege DX, and when I got it the harness was cut as well.
The wiring for mine is as follows:
CONSTANT POWER = Blue w/ Red Stripe
SWITCHED Power = Blue w/ Black Stripe
Ground = Big Black wire
ILLUMINATION = Red w/ Black Stripe
Left Rear (-) = White w/...
Something to check is the connection to the alternator; look at the alternator, and make sure the wire's bolt (take off the plastic cover) is screwed in all the way. This can cause the room fuse to constantly blow (it happened to me), and the alternator to eventually not charge the battery...