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[1jzdreamer]

Sounds like the starter solonid stuck in the on position and the starter kept cranking till the battery was dead. I would either go to an autowrecker and buy a used unit as they aren't common to fail and this will be the cheapest alternative, or get a new unit (bosch or denso make good rebuilt starters, from a auto parts outlet). if the solonid stuck while you were driving, you probably over spun the starter and cooked the brushes and the bearings, and that would be why it was smoking. While you were driving air was going by it and the smoke wasn't obvious.
The insulation on the wiring may have melted at the starter so when you remove the starter, it should be obvious. I wouldn't think this happened but you never know. Id get another starter and deal with it on a case by case basis. Replace the starter and if the wiring is fine, then your good to go. Swapping the starter shouldn't be more then a 2 hr job. I have done mine in 30 min before.
I wouldn't worry about the flywheel/flex plate unless the starter wasn't engaged while you were driving, and tried engaging while you were driving. Then when you pull the starter, look in the hole (where the starter pulled out from) and using a flashlight, inspect the teeth on the flywheel/flex plate. If they are ground up horribly with teeth broken then you probably will want to consider replacing it, but I doubt you will find much wrong.