First off: check out the
2C-B Aftereffects/Side Effects thread. You'll find a lot of other users' reports there and it's a good place to share your own.
I've never used 2C-B myself, although I have quite a bit of experience with 2C-I and 2C-E. A few general notes:
-As a research chemical, there really isn't much definitive/authoritative info out there. There haven't been extensive studies of the effects of use with 2Cs like there have been with, say, LSD. 2C-B got some studies in during the 70's but not a ton. Most of what you'll find is other users sharing their personal experiences.
-Headaches and muscle soreness are both quite common side effects of drugs in general, and particularly stimulants. 2Cs tend to be fairly stimulating.
-As for tolerance, that's a very complicated issue with psychedelics. It varies enormously from person to person, from compound to compound, etc. Tolerance probably played a role in diminishing your second trip a bit, but it's not typically associated with physical side effects, just a less intense trip. Certainly I wouldn't expect two doses within a few days to cause any significant side effects that one dose wouldn't have caused.
How much did you take each time? You use adjectives like 'huge' and 'splitting' so I'm guessing these side effects were pretty severe? Do you get similar side effects from any other drugs?