However, I am not certain about protocol 3000. Is that just using spray of MMS1 and DMSO externally only using spray bottles?
Yes, two spray bottles. One for MMS1 and one for DMSO. If you have an animal feed store near you or a store that sells similar products, they should carry liquid DMSO. If you can find it there, then you don't have to wait for it to arrive in the mail.
Looking in Jim's book I am directed to page 303 from the table of contents. I am looking for animal skin spray dosing information which turns out is the same as for humans. I am directed to page 76 where I discover that the standard dosing formula is 10:1, 10 activated drops of MMS to 1 fluid ounce/30 ml of water. Dosing consists of spraying from the bottle containing MMS1 followed by spraying from the bottle of DMSO. No ratio is given, so I am going to guess it is equal number of sprays from each bottle. You may want a third spray bottle with just water in case you need to dilute the solutions you just sprayed.
You can dose MMS1 activated orally and MMS unactivated in her water dish. Since you are dosing 3.5 ml of MMS1 solution (cup 2) hourly for 8 hours, that totals 28 ml/day from an available 120 ml of solution. The original solution was made from 8 drops of MMS which can contain a maximum of 54 mg of CLO2. (each MMS drop contains up to 6.7 mg of CLO2.) So, orally dosing with MMS1 she gets about 13 mg of CLO2 daily. Two drops of unactivated MMS would contain about the same amount of CLO2. You could add 2 drops of unactivated MMS to her water dish.
Since you have not seen any improvement so far while using MMS1, increasing dosing might be the next step. Adding MMS to her water bowl would be an increase of twice the amount of CLO2 daily she is now getting. If still no improvement is seen, then increase oral dosing. You can also add DMSO to oral dosing as in Protocol 1000 Plus.