Duane, I used to hike quite a bit on the FLT, North Country, Conservation Trail and the Bristol Hills Branch of the FLT when I lived in Western NY and then in the Finger Lakes Region.
(Conservation Trail shares the FLT in NY's Southern tier and then heads North near Holiday Valley Ski Resort to the Bruce Trail in Canada.)
I am trying to figure out where there are other trails to do a loop. I cannot recall anything between Watkins Glen and Salamanca, which are the areas I am very familiar with). I can check my maps this weekend, but I beleive everything is linear.
Being from PA, you are probably already familiar with these trail, but I thought I would throw them in:
If you are dead set on a 3-day loop, have you considered the Black Forest Trail (BFT) in NorthCentral PA 42 Miles, strenuous and very doable in 3 days.
You could use several link trails and do a section loop on the 83 mile Susquehannock Trail (STS) which is also in North Central PA, just west of the Black Forest Trail.
On the east side of the BFT is the West Rim Trail (WRT)- 32 Mile Linear Trail, however, Chuck Dillion at Pine Creek Outfitters at the north end will give you a car shuttle for about $35.
Just east of the WRT is the Old Loggers Path - A remotish 30 mile loop which is also very scenic.
Finally there is also the remote Quehanna loop, (SW of the STS) but I am not sure if there are links to make shorter loops (IIRC, it is around 72 mile loop ).
If you aren't familiar with these loop trails and would like more infor, please PM me and I'd be glad to give you as much detail as possible.