I like "The Explosive Child," also, and while it's not specific to PANDAS, necessarily, one of the authors has worked with Dr. Swedo in her research at NIMH, so he's at least familiar with PANDAS presentations.
I'm not sure it matters whether the disrespectful behavior is uncontrollable because of PANDAS, or if it's uncontrollable because your kid is so far out of his self-control that he can't stop himself from blurting out rude words or making rude gestures or whatever. I mean, yes, PANDAS can definitely mess with your executive functioning and make it more difficult to display age-appropriate behaviors. But most behavior of that kind comes from a lack of self-control, irrespective of the genesis of the lack of control. Either his brain is physically impacted so he acts out, or his "mind" is emotionally impacted so he acts out, the results are the same. And maybe the same tactics are applicable for the behaviors, as well. "The Explosive Child" has some great strategies you could try, but as I recall, pretty much all of them suggest that you de-escalate any unpleasant exchanges by dis-engaging, taking a few minutes to calm down and dial everything back, and then re-engaging again in a calm, controlled tone of voice and body language to resolve the dispute. Seems to me that could work whether PANDAS or non-PANDAS.
I personally think that pretty much ALL non-age-appropriate behaviors (meltdowns, tantrums, etc.) our kids may display during this illness is at least partially -- if not wholly -- attributable to the illness. But then again most "normal" kids will test their limits during the natural course of growing up, too. So, in your shoes, I might ask myself, "Is this behavior I could expect to see out of a 'normal' XX year old?" If the answer is "yes," then maybe you deal with it as you would with any kid behaving that way. But if the answer is "no," I think you still address it, but maybe with a little extra compassion and patience, adding into the discussion something along the lines of, "I know that you're feeling especially out of sorts right now while we get the inflammation in your brain and the other PANDAS stuff under control, but you have to know that speaking/acting that way is still unacceptable. Let's try and brainstorm some things you could try instead of yelling at me/your dad next time you feel this way."
My son hated being told he was not acting his age when he'd meltdown over something pretty minor or lose his patience in 0.2 seconds during his PANDAS. But I've got to be honest; I didn't do it to be cruel, but I felt like it was somewhat important that I hold a mirror up for him because I didn't want him to dig a deeper and deeper hole for himself socially. I wanted him to have some outside perspective as to how his meltdowns looked to his peers in the hopes that it would give him some incentive to work with me on some of the "Explosive Child" strategies for dialing things down so that he could "save himself" in some of those outside world situations. It was tough, and we weren't always successful. But I do think it helped him maintain some perspective, especially when he got out of that intense moment and could look at things a little less emotionally.
All the best to you!