tree roots as a way of speeding up cycling?

I'm not sure about the tree/plant root thing. But it does seem to me that unless you rinsed it prodigeously you're risking introducing all sorts of nasties to your tank.

As for the pH, my guess, not knowing anything else would be ammonia.

NH3 + H2O = (NH4+) + OH-

Which would raise your pH. Did your ammonia go up as well?

Just so you know. Flying foxes do not do well together. At fisrt they are fine but I had 2 in a 20 gallon and had to move one out do to the fighting that was occuring. They are pretty solitary fish.

A 110 may give enough space for them to coexist. The 10 and 20 gallon tanks have small footprints and so not enough room. The SAE's (ture not false) are the ones that generally coexist the best.

I have heard before that to increase cycling in an tank, put a couple of plant or tree roots into the water, as the roots contain all the necessary bacteria.

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There may be some confusion on this issue or the way it was presented to you, Aquatic plants will speed up a cycle significantly, and most of the bacteria they introduce is in the roots, potted plants are the best because the fibre potting material that the roots are in is an excellent source of bacteria, Adding tree roots or plants from a non aquarium source I wouldn't think would help much at all and as was mentioned, they stand a good chance of introducing some nasties into the tank. If you do cycle with live plants do some research, partial information could get you some serious algea problems, I came real close to learning this the hard way, and am still not clear out of the woods.