I try the deep breathing and relaxation to calm it also. It doesnt seem to help me either.
Well, I'm no expert, but I've heard/read the same stuff you have - that lesions in the brainstem can disrupt those autonomic functions.
I have two lesions in the brainstem. Every once in a while, my heartrate will be high (90 to 120 bpm) for no reason at all. I work at trying to bring it down with deep breathing exercises and relaxation, but it doesn't seem to help. I also have an occasional irregular heartbeat, and shortness of breath upon standing.
I haven't brought this up with my new neuro. My old one thought that those symptoms weren't related to MS, and blew me off. I'm going to talk to the new neuro about it and see what she says.