I put in a lengthy legato practice session last night, but nothing out of the ordinary from my general practice routine. This morning I woke up with a lot of stiffness and a little soreness in the "thumb pad" area of my fretting hand. It's stiff/sore on kind of the heel of my hand, near where the thumb muscle connects to the rest of the hand. This has never happened before. Should i be concerned? How long should i avoid playing for?
Sounds like you've been using poor technique, and way too much force. You don't need to apply a lot of pressure to the strings. I think you've probably been using your thumb to apply the pressure instead of your fingers. It's a very fine line between them, but it can make a lot of difference. Plus you might have your thumb in a bad position. Take a few days off, go see a doctor, and when you've healed, try it again. If it still hurts, take some more time. Just make sure you're playing properly, or you may end up hurting yourself again.
I suppose when practicing legato stuff, you're fingers get tired and you probably compensated by increasing the pressure with your thumb. Probably gave those muscles a bit more of a workout than they're used to and they're a tad sore this morning. Maybe just take a day off from practicing if you feel it's necessary and then see how it feels tomorrow.