Two things, most drugs for anxiety have a cumulative effect and it actually takes time for them to be effective. At the same time, when coming off the medication it should be gradual halving the dosage, then halving it again before discontinuing it over a couple week period.
The other part of this is your boy definitely needs to do a 2-3 week quarantine in the spare bedroom you mentioned. Spend plenty of time in there with him, he just needs a space to take ownership of and truly feel safe. My guess is that he is constantly walking around on the defensive and as someone else mentioned probably some scents that are keeping him on high alert.
A lot of this sounds similar to our boy Kebu several years ago when moving into a new home. Although not armed with all I know today, I'm pretty sure with a quarantine period the things that took forever to resolve could have been done in the first months.
Lastly, what is the body language suggesting? Tail up or down, ears back, tail fluffed? The ears are the best sign and some notes would help figure out what's troubling your boy.