If you are following Protocol 1000, you are probably making up an all day bottle with an 8 drop dose of MMS1 for 8 hourly 1 drop doses .
Try reducing dosage to 1/2 drop hourly doses and see if throat irritation goes away.
If you still have throat irritation with 1/2 drop doses, then let's try using unactivated MMS and let stomach acid do the activation.