I do 100% water changes every day and I've had him for about 5 days.
That's to much for a betta in his situation,
Leave him in the tank and do no more then 50% water change per day, with as little disturbance as possible,
Your over stressing him along with everything else,
The best thing he can get from you is peace and quiet, be disturbed as little as possible and most important the BIGGEST body of water you can give him,
This guy sounds like so many I have been given and brought home,
Clean cycled water, the bigger tank the better, peace and quiet, is the best you can do for him. and then as he comes around more some good food.
Really this guy needs a much bigger tank.
Some bettas that have been in those small cups to long will never totally get better, Their only real chance they have comes from a bigger tank.
As for the Javex, you've had him 5 days and doing 100% water change,
I doubt javex is an issue now if it ever was,
His problems sounds like so many others, these small cups/containers are the cause of his condition,
Also if these two fish are still together you need to separate them ASAP!