I wouldn't worry about "Stubby", Rob. Squirrels tails are not prehensile and don't have much to do with their agility. They are too light to be used for balance. They are used mostly as communication tools and to attract mates. If anything, he just won't get laid as much the squirrels with the longer appendages (isn't nature universal?  ). My property is full of squirrels of all sizes and colors and they all do just fine. I even recall seeing one with a short tail.
Just do what you can and release them with your best blessings. Let nature do the rest. You'll have already given them more than they would have had. 
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Pearl '92 LS-L 179K (Historic 1st 5-speed SVX)
Mods: 5-speed, 4.11's, Group-N motor mounts, dual Magnaflows, cone air filter, Kenwood MP-228 CD/Receiver, white-faced gauges, '97 grill, custom window tinting.
Ebony Mica '92 LS 80K Oct 2002 - Dec 2004: Victim of theft. She served me well.
You can tell the lack of craftsmanship by the wrinkles in the duct tape.
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