Hi Bronxmom, (Wish I had the time to edit this down!)
I have a son with PANDAS. After experiencing seizures with the presence of strep throat, he is now on antibiotics twice a day. He was diagnosed with PANDAS at about 10 years old, although our pediatrician caught it at 4yo as an affect connected with strep. We didn't get to treat it aggressively until later.

Anyway, my son just turned 16. He did have trouble writing and even walking after each seizure, but other than soon after the seizures, he never gave me any attitude or behavior problems.
With the weak tone in his hands, I had him dictate outlines to me, then later he would write the main ideas, and I'd write his more detailed ideas down. Later, the main ideas turned into sentences that he wrote. Eventually, the other details were added at each level of outline.
BTW, I had an IEP for him through PANDAS, to allow this. I'd advise you to do the same for the reading log and journal work. Have him start with just an outline for the journal. Tell him (if the teacher okays this) that you and the teacher made another choice for him to make. He can do it like all of the other students do, or he can work really hard at making an amazing outline with good vocabulary words that you will write for him while he dictates what to write. He'll work hard on it then and see it as an equal alternative. Have him first start with a title, date, then each week or so, hold him accountable to write a little more.

Worksheets that distinguish between good and better writing also are helpful. My son had to simply check the sentence that was better and pick the reason why. He had several objective writing programs he followed. Some fill-in-the-blank. He also did "Editor in Chief" editing programs on the computer.
When he couldn't write, he read a lot to compensate and fill up the time, picking books only from the Great Books list from Adler.

Overall, I think the behavior issues are not related to PANDAS, just based on my one son's experience (which is therefore not valid smile ).

The main thing isn't to worry about grade level, or grades on a report card, but to consider if he is learning an appropriate amount about writing. If he isn't, then help the teacher find some methods to accommodate. HWT was a handwriting program he did, but I can't say it helped tremendously. When experiencing multiple seizures, each time you kind of go back to square one, and well, the enthusiasm of the program (if there ever was some) wains. It is understandably frustrating to know that you already knew how to do this and went through the program, but still have to go back and redo it again! This is where PANDAS/seizures cause some attitude problems, but I don't believe that it warrants major behavior problems, if the program has been modified appropriately.

BTW, my 16 yo has been attending a state university, and just this past week we found out he was admitted to a private university full-time as a regular student. I say this to let you know that if you stick to it (don't give in and throw writing out of his academics), and get his behavior so he can learn independently, most likely everything else will be okay!