Sounds like a good strategy. There's a lot of new trail since the Andrea L book came out. Some of what she has to say makes good sense. There are some sections you would be better off to avoid. But with a lightweight modern bikepacking kit there's a lot of great riding you can do.
A quick blow by blow North to South.
From the state line you will have to climb a fair bit on mostly good trail.
Good trail all the way to the Canyon. There is one section that has been closed for years due to fire easy to hit the highway and get around it.
The rest of the way to Flagstaff all good trail with some dirt roads.
After Flag the trail does get a little rough but not too bad.
Good riding gets you all the way to the Mogollon Rim
http://en.wikipedia.org/wiki/Mogollon_Rim It's a big down to get off the rim.
After the drop down the AZT turns to shit on the oldest most eroded section of trail. The Highline trail was built for mules in the 1880's. Just head South on the road to Payson.
The AZTR uses a quick route mostly dirt close to the highway south of Payson. At this point taking the AL route will be more scenic.
After Rye the red route will be hard, it adds a lot of pavement but I would say just take the easy route along Roosevelt Lake and the dirt road (Apache Trail) on to Phx.
After Phx you actually only need to go into Apache Junction east of Phx. There is sweet new trail heading south from the Picket Post TH.
Good trail mostly ride-able all the way South to Oracle. As I mentioned earlier for South bounders I would go up the dirt road (Control road).
Once you get to the top of the Control road you are up high in the pines. There are trails that get you off of the highway but most are real techy. Better to take the highway, if you want a break from the pavement take the Bugs Springs trail. Some hike a bike but lots of fun down hill cruzin.
After Bugs Spring trail you can rejoin the AZT at a place formerly called Prison Camp.
After Prison Camp the AZT is good fun trail for 3 miles to Molino Basin.
After Molino the AZT head east up and over a pass lots of hike a bike even on the techy down hill you'll walk some. This leads out into an area of good trail. But is out of the way and you could just as easily head down the highway and be in Tucson in minutes in stead of hours.
After Tucson there is great new trail all the way to the forest boundary. At the forest the trail get tougher but not that much tech. There is good riding all the way to Kentucky Camp and beyond to Gardner Canyon.
After Gardner the trail goes back into Wilderness so no bikes. You can bail to the highway at several points along the way. Or get all of the trail some of its very interesting old flume trail left over from the mining days of K Camp. Look at the AZTR course to see a good way to get from Gardner out to the highway.
After Gardner how ever you go you end up in Sonoita.
From Sonoita you can get to the Border pretty quickly on the main paved road to Parker Lake and then dirt to the official AZT ending points.
The last two passages Canelo Hills West and East have a lot of tough riding in them but it's cool rugged country. Unfortunately there is a lot of smuggling in this area and some trash as well as a lot of unsigned trails.
Patagonia is the last town for you it is on the official AZT route and is worth going out of your way to get to. More for it's interesting history and great pizza at the Velvet Elvis then for any good riding you could add.
It has been done before to just head South from Patagonia to a little border town called Locile but there's nothing there and you would need a pick up.
From Patagonia you could just roll the highway to Nogales where you can likely get a shuttle to Tucson and eventually back to Phx.
If you still have time after P town and choose to head east. The Canelo's are worth doing if you are still up for more pushing. You could just take the AL route on roads and go all the way to Sierra Vista and likely get a shuttle from there.
Flights book, cool. Your in for a great adventure no doubt.
Hopefully all of this will make sense when you are looking at the course.
Tim