Sweetie, you are not nuts. Every mother to a Reflux baby is a supermama IMO!
If you have any concerns that he is in discomfort I would take him to the ped. as soon as possible. Usually your gut feeling is not mistaken.
We can tweak things all we want but if he is in pain then no amount of tweaking is going to help, yk?
I do think he will outgrow the going into the crib sleeping, I have seen DS do that. I took a while, but I didn't mind at all, because he was sleeping.
It does seem to me like his morning is messing things up. I know that you think the morning is ok, but he is doing an extremely long A time first thing in the morning and is probably giving you an OT nap. After that it's very hard to get things right again. So IIWY I would work on shortening the first A time, something like 1.5h maybe and see if that helps.
Many babies needs their first A time to be shorter than the rest of the day so if a week of 1.5h A time in the morning doesn't help then maybe he'd need even less that that.