Ahh...I know that feeling of being a New Mom and EVERYTHING - could be a cause for concern.
This instances sounds like it might be 'reverse sneeze' or a little gagging from dust, or inhaling water or food. I *think* he will be ok. Just keep a close eye on him (hahahah ~ which I am sure you are already doing

)
I tried the crate in the beginning - they have been sleeping in bed with us for 3.5 yrs now - so you see how far the *crate sleeping* went ~ just part of being 'owned' by our Yorkies...I guess...
Welcome to YT - You are gonna LOVE it here