Okay, so the sneezing with testing that AO joints could be due to your hand position over his squashy little Boston Terrier face while assessing flexion / extension etc. I originally had thoughts about whether it could be correlated to the possible disc lesions, but I don't think so.
The increase in tone in the neck makes sense to me in that if there is inflammation from the discs pushing on nerve roots or disc degeneration that causes secondary pinching of nerve roots, you can get an increase in tone. Alternately, simply spinal cord lesions that result in upper motor neuron damage creates increases in tone. So, if the neck isn't painful, I'd go with either option #3.
The change in the bowel function / awareness is likely a progression of his autoimmune spinal cord ischemia. Same with the CP deficits and weakness.
In a case like this, or rather, a case with this diagnosis, you may see various iterations of lower motor neuron signs and upper motor neuron signs, depending on what part of the spinal cord is currently under attack... or where and how the disease progresses. Motor cord body lesions at C5-T2 can show LMN signs in a front leg and UMN signs in a rear leg. Motor cord body lesions affecting L5 - S1 will show LMN signs to a rear leg and maybe UMN signs for bowel and bladder.
It might be worthwhile to teach the owner how to be proactive about a bowel routine, and how to use a Q-tip to stimulate the rectum and get any poop that's 'sitting at the back door' to be expelled at regular times. It's not fool proof, but it might reduce the incidences of 'in-house fall-outs'!
I hope this helps!
Laurie