Blimey Daisy, that sounds awful. Glad you're on the mend though 
Is TT related to reflux?
Cut the dairy out for a few days? he may have an intolerance to it. Ds3 was always a little bit sick after yoghurts when he was weaning. I cut them out for a few months and Then when he had them again a few months later he was fine.
UBW - don't blame yourself that he is small. That just may be his frame. Trust that he is eating everything that he needs.
do you defo know that he is eating very well at the CM and nursery? Also, what is their definition of 'very well?
Something I often do is put less on the boy's plates. I think sometimes a full plate is overwhelming to them, and then if they do clear their plate (even if it's only a small amount) everyone is happy.
Also both of my boys eat the least amounts for their evening meal. So, I limit drinks in the afternoon (they would rather fuel themselves on squash and milk given the chance), do the small portion on the plate thing and trust that if they hardly eat then they aren't hungry.
I also said this on here not that long ago, but young children can only control two things in their lives. What goes in and what comes out. Both of which can turn into a real power struggle - as you will find out when you start potty training 
I hope some of this helps. Eating, or lack of, is such an emotive issue. It's one of the ways in which we nurture, so when it goes awry it's easy to get upset about it. But like you've been doing, don't make it an issue and it'll come right