Harpers Ferry to Katahdin is half the trail. I did it, and it is nice because you are out there for 3 months or so. That was enough for me at that time. Others do the trail in thirds, roughly either Springer to Pearisburg, Pearisburg to Bear Mountain, or Bear Mountain to Katahdin. The choices are yours.
Conditioning? The best conditioning is backpacking itself. So, on your daily walks, put on the backpack with 30 pounds in it. Other good conditioning is running and biking. I have always felt that biking was good for the knees. Almost anything that gets your lower body moving and gets your heart rate up is good conditioning. Some climb stairs with a pack on. Others use a treadmill with a pack on. The main point is to do something rather than sit on a couch.
Where and when to start? The options of where are limitless. People start or leave the trail at almost every road crossing between Springer and Katahdin. When? There are some things to avoid if possible. First, Katahdin basically closes in mid October. So, if that is your goal, you need to be there well before hand. Also, in Vermont, New Hampshire, and Maine, expect frosty mornings anytime after mid September. Likewise, in June, the streams in Maine are still high with snow runoff, and black fly season. So, I would avoid New England in May and June. Starting at Harper’s Ferry in May is good, because you will be with the earlest of the thru-hikers. These are the guys that weathered the winter storms down south.
I wouldn’t worry about finding good people to hike with. They will discover you along the trail.
Peaks