hmm.....did you check for continuty between the starter soleniod wire and the ignition switch? perhaps thats the wire u are talking about, I am not too sure which pin it is. And also definitely another thing to look at is the alarm ignition kill. Usually any good alarm will use a fail safe relay, which means incase the relay doesnt get any juice ur car will still beable to start, but you never konw.

From what you have described it seems its an open wire somewhere in the harness, because the starter works fine.