This is common. I have my son on the 3 day on 4 day off, the regression is still there, but not quite as bad as the other protocol.
One thing you could try is Epsom salts baths or MSM. They both seem to help my son during the off cycles. Another thing that has helped him recently is Cranial Sacral therapy weekly and some that we do at home.
My son has a very rapid heartrate, hugely dialated pupils and slightly higer body temp while chelating. And the therapy helps to bring all these down.