This was me, too. Tom got glasses at 2 1/2. He'll be 6 in November. We started gluten-free mid-February this year. We weren't fully GF until.... mid-March? (It was getting GF vitamins that was the "final" stage.) I remember not long after going GF, he was taking a bath (with no glasses) and he looked up at the ceiling. His eyes used to always go in a smidge when they were looking up. They were sooo straight looking. I remember staring at them, fascinated. (Probably what you did when Spencer first had surgery.) I was originally told that the glasses were just to straighten his eyes. They seemed to do sooo much more, but that's why they were prescribed. So, if the glasses were to straighten the eyes, and going GF helped his brain straighten them, does that mean the glasses are now pulling them out? (I'm not really asking you, but this is what I've been wondering myself.)

The other thing with some of these allergens (dairy, gluten, and other biggies that are consumed daily), is that they affect the absorption of vitamins and minerals. So, is it the allergen? Or just the lack of certain vitamins and minerals in the bloodstream causing the problem?
So, yeah, I guess I do think diet can affect it. I've also noticed "side-effects" of Tom's vision since going GF. He doesn't seem to run like a toddler anymore, in the sense that his legs are not spread in a wide stance (in the shoulder-to-shoulder direction), although he still runs very slowly. He's judging steps better, especially when he's running (running across the street, and jumping up the curb). And, he's actually jumping a little bit while running (instead of tripping over the uneven sidewalk). He doesn't fall as often.
I'm not trying to give you a hard time, either. I completely understand what a pain in the rear it is. I'm still feeling overwhelmed from our GF decision, and wondering why I volunteered to teach Sunday School, and why I joined that church committee and now have a three year commitment. We used to eat out for supper every weekend and that was the HARDEST to give up. Cooking on weekends?!?! If it helps you any, I'm trying to cook double for supper at night, so that we can eat the same thing for lunch the next day. When I'm really on top of things, I even put Tom's lunch in his Tupperware container while I'm putting the rest of the leftovers away so that it's ready to go in the morning. (It doesn't happen as often as it should.)

I'm glad you're going to make his lunch tomorrow. (Misery loves company, and all that.) Given your allergies and his history, I think messing with his diet will do a lot of good. Go, Bec! Go!