It could also be something entirely different. You say that the feral mum had disappeared and left him behind. Perhaps that was for a reason??? They very oftne know long before we do that something is wrong with their young... and we have had it happen many a time especially with ferals.
They will leave their young and move the rest that are stronger or healthy or try to kill the one that is the weakest or leave it as prey for predators and move the rest to safety. Perhaps this little one has some form of brain damage or has not developed properly. You never know. It could be that the fits are completely unrelated to the Chlamydia or the vaccination.
Also just out of curiosity. WHen the little one took the chest infection / respitory problems did the vet use Baytril to treat at all?? Just ask our of curiosity as we have had a couple of kittens that when this scenario has happened have been left with fitting and weakness in limbs as well as lack of co-ordination. Even in small doses it can cause such problems.
Don't know if this helps much but there may not be much that can be done I'm afriad Sam. Good luck in passing this on tho... hope the little one finds peace one way or another soon xx