Starting Procedure going into Protocol 1000

Hello from the Washington State,

I'm looking for guidance with going from the Starting Procedure to Protocol 1000 and have 2 questions.
1)  I'm not understanding why Protocol 1000 starts with a lower dose than the highest dose of the Starting Procedure.
2)  Going from 1/2 drop to 3/4 drop today, my dog has diarrhea but doesn't seem sicker than he was.  Should I stay with 3/4 drop?

Thank you very much~