Coincidentally I too have been trying to figure out where the GWT goes. I have ridden a few pieces of it and we are planning to ride another section around Flagstaff this spring. I have been finding conflicting info on where the trail is. I first tried placing waypoints at known roads using the "notional" maps on the official website.
I recently discovered that the Arizona Benchmark map has notations "GWT" along the trail. Unfortunately they are fairly sparse and it is not always obvious how to connect the segments - especially where it crosses I-17 somewhere between Bloody Basin and Camp Verde.
Anyway I attached my planning file which shows the sections in soutern AZ and Utah where I have ridden it. It also shows the planned route for the spring ride, all the waypoints I have conjectured. I used the Benchmark map routing which seems to be east of the notional map.
BTW the offical GWT seems to follow 89 for 100 miles getting across the Colorado River. The track marked Navajo Lookouts, which I got from some ride report looks like a far better way.
Well even though the file was well under the size limit I could not upload it. I will post it on GPSExchange in a day or so.
If you PM me your email address I will send it direct.