Help me bees, I am out of ideas.

DS has been pooping very frequently for about a month now. Since he poops all the time his butt is so red and sore between the cheeks where the poop sits. Some days the rash is terrible acid rash but most days it's just red. We're washing his bottom and using Triple Paste (daycare) or Desitin, and Aloe (doctor's recommendation but makes LO scream, maybe I picked the wrong kind) at home.

Daycare is doing their best (rinsing, not wiping. applying ointment, frequent changes) but nobody can keep up with constant diaper changes. I've stayed home from work to try and I can't even do it.

I'm out of ideas of what is going on and what I can do to help. I took DS to the pediatrician last Friday and she thought it was a virus. I tried to be patient and wait it out but it's gotten better and worse again since then.

Theories I've had:
Constipation: I was treating it like constipation since LO cries and bears down when he poops. The poops aren't hard, they're normal to soft brown. Just frequent and small. Consistent prunes, pears, extra water - hasn't helped.

Food allergies: He's mainly BF and getting a bottle of formula 1x a day. We introduced formula shortly before this started. I want to try cutting that out but I'm worried swapping with milk will make things worse instead of better. I cut out eggs for two weeks since LO1 was sensitive to them. It has gotten better and then worse again since that time so I am ruling eggs out.

Rash pain: Could his bottom be so irritated that it just hurts to poop so he stops himself?

Teething: LO got his first two teeth about when this all started. He seems like he's going to get the next two very soon.

Anyone else go through this?