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From time to time over the last decade (both before and after cancer) I have felt little bumps under my arm. When I point them out to my doctor he will say "oh, that's just a lymph node". So apparently they can be felt sometimes even when they aren't acting up.
The other thing is radiation. If you had radiation, it might be responsible for some twinges and weird feelings that come and go. I have read that this could happen for quite a while and I experienced a little of it myself. So maybe that is part of the problem, and it will get better with time.
Let us know what you find out.