I did not adjust the searing stem just the rebound dampening force adjuster thats on top of both forks ( the one with a black plastic nob that can be turned by hand, i did not use any tools to do this)
Put the damping adjustment back to where it was before you noticed the shake. Also, are you sure you have the right and left adjusters at the same position? A lot of bikes shake a bit on deceleration. There are a lot of factors involved in why a bike might do that, but there is a chance that your adjustment induced it.
The best way to troubleshoot, is to change one thing at a time and see if it makes a difference. If that change doesn't, put it back the way it was, then try another change. I would put your damping adjusters back to where they were before you adjusted them.
I highly doubt the weight difference of the muffler would cause it. I can load my bike, and not have any shake, and unload it, and not have shake. the same holds for carrying a passenger, so the small weight difference of a muffler should make no difference.