I can't help you with the upper stretch, but years ago I canoed from Emlenton to about 10 miles above Pittsburgh in a three days, just sort of loafing along. I also used to spend a bit of time on stretches farther up, but nothing that connected a whole thing the way you want to. It ought to be a fun trip -- that's beautiful territory, especially the part in upstate PA.
Think about timing it out so you don't have to try to find a camp too close to Pittsburgh. It's pretty well developed along the river there, particularly below New Kensington. Banks down there can be steep and very rocky, specially if the railroad is right next to the water, as it often does. Many of the islands have summer cottages on them, so what looks good on the map might not be so good in reality. Maybe Google Earth could give some shape to your thinking about how to strategize on that score.
Be aware that at some point you'll start running into locks and dams on the lower section. I don't recall how many in the section I did, but for a fact there are two in just the stretch between Pittsburgh and New Kensington. Locking is not a big deal, it's just time-consuming under even ideal circumstances. You may not have the option to portage because of the way the Corp of Engineers have their sites set up.
Also, there can be significant delays in locking through because of barge traffic having priority. In most instances, they're not going to let you go through with barges, so you sit and wait. And if it's a long "tow" they have to split it in two. I've waited an hour and a half on the Mississippi in that kind of situation.
Hope this helps.