He could have gotten parasites from live feeders, that is definitely not unheard of...
Protozoans are another possibility, but those are usually found in imports/wildcaughts or reptiles from dealers that house imports/wildcaughts. However, back when I did rescue these infections were found in a few of them.
http://www.reptilesmagazine.com/Flag...estinal-Tract/
They are treated with different medication then internal parasites.
Be careful not to crank the heat up to much on them, they usually get quite unhappy and cranky when to warm. Try to get the temps perfect and then raise a couple degrees..