Regarding the break-in period, as Roger said you can allow for it with decreased mileage initially on your thru-hike, and your training can incorporate a lot of smaller trips (looooong day hikes turn into overnights which turn into weekenders into...).
I live in Tahoe so I do quite a few overnighters with my dog if I don't really have anything else going on (we hike out our front door, so this can be any night of the week). My wife and I try to do one thru-hike a year, but after the AT, PCT, CDT, CT, etc, we now seem to focus on 200-400 mile hikes in cool areas we haven't been to before.
We're now of the mindset that we'd rather go to a really cool area in the perfect (mild/no bugs/dry) season instead of doing a thru-hike that puts you in areas you don't necessarily care about in the wrong (hot/buggy/wet) season.
edit: we don't like to go more than 10+ days w/o resupply.