I have never dealt with diarrhea for that long on my baby, but we have gotten some BAD rashes associated with it before. There seems to be some stomach bugs going around right now. Sometimes they get better and then re-activate before you get completely over them...
I made a home-made diaper spray with chamomile tea (a little over 1 cup) that I boiled for 5 minutes-I added 1 teaspoon sweet almond oil, 5 drops of lavendar essential oil and 5 drops of tea tree oil for germ killing and fungus and put this in a spray bottle after it cooled-smells nice and cleans well and isn't sting-y. Important for healing. Got the essenial oil/almond oil from sprouts. You could put this in a jar and dip cotton pads in it if you didn't want to go the spray route.
Also, I use neosporin ointment (not cream) once the bottom's clean-the ointment sticks better. Then I go over it with vaseline to seal out the poop so it doesn't get back into the sores.
I am so sorry, I hope your poor baby get's well soon!