Been there many times. Only cure is rest and take a gym break. As for the thumb, I have that too and have had it for about 10 years now. The cause is tendons that were torn and never delt with properly therefore it never healed right and tends to remind me of that every once and awhile. As tuff as it is to take that break, you have to realize that once you enter the over trained zone you're doing abosolutley nothing in the way of building muscle or for that matter any gains in any area at all. Your body will just keep feeding off itself and eventually break down.
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