Since we have neither a medical history nor diagnosis, it is hard to say.
6 drops an hour, activated, of MMS is a fairly high dose (although I've known others to go higher - but those kinds of dosings are usually for people with a life threatening disease - and we don't know if you have that). The pain could be gas, it could be parasites, it could be a herx reaction, trying to remove toxins that are more than it can handle at this stage of the game, it could be any number of things. I've had upper right quadrant pain for 15 years and have been told it's "referred pain from my DJD" - degenerative joint disease.
MMS1 and MMS2 should not hurt the liver. The only thing in the protocols that might affect the liver would be DMSO. If it were me - and I can't tell you what to do - I would drop back to the max 3 drops an hour for 8 hours a day and stay there for a while. Let your body detox for a bit, and do it slower than the 6 drops an hour. Build back up, but only at a drop an hour, and stay a couple of days at each drop. You have time to do this if you do not have a life-threatening illness.
Then when you finally do add in the MMS2, again, do it slowly. A few granules at first, gradually going to 4-5 capsules a day (one every 2 hours). The dose will be half a size '0' capsule, ultimately.