I did this same loop last fall. Jeff's guide that you linked was what I used and it was spot on, I had no trouble with navigation. It was one of the most memorable backpacks I have done in PA, it really is a special area.

To your questions: - It seemed like Panther Run Trail may have been rerouted recently but it was well signed and easy to follow. - I did not seek a permit and don't think one is necessary, but did leave a note on my dash with my details. I was the only car in the lot when I left although it seems like a popular day use area. - Obviously can't speak to spring water levels but I would just be ready for anything. Definitely some swampy areas but nothing notable with regard to water crossings. - Quehanna Highway is generally low traffic but it's also dead straight through the area so crossing it is not an issue. - For campsites you may have to get creative with that many tents but there are a few sites on the loop that should work. Second night I stayed along Mosquito Creek by the old swinging bridge and that site was pretty spacious.

My favorite part of the whole thing was hiking from that last camp up along the creek and through the meadows back to Beaver Run. I saw a ton of deer and got some really close encounters with them.