I also had a son with acid reflux problems. He was on medication until he was 9 months. From what I understand the problem may never really go away completely, but become more regulated due to the digestive system maturing, etc. My son is 14 months and still has issues with certain foods. Citrus should be ok for his age, but he cannot tolerate it, so even though the problem isn't evident, don't discard it completely.
Secondly, on the sleep issue, my thoughts are exactly that... he's just so cozy in his seat he's not waking to eat. God bless if your son is at least tolerating the crib. I think he wakes in the crib because he hasn't yet learned to comfort himself to stay sleeping. A little perspective - my son wasn't in the crib until 6 months and only started sleeping thru the night (7 hour stretches) at 12 months - I learned that it was actually my fault - I was feeding him when he woke even at 12 months (and I was also 7 months pregnant - not the time to be losing sleep myself). We had to do a few days of sleep training (strategically letting him cry it out and learn to comfort himself with reassurance from us - he also didn't know how to fall asleep on his own) when the doctor said 'it's time to drop the feeding - he doesn't need it, he's just manipulating you'.
In essence I think it's important to put him in his crib and teach him those skills early, and tolerate the one waking in the middle of the night, until your doctor says it's ok to expect him to drop it and push for a wake free sleep. Good luck!
~mommy of 4: 12 & 10 yr old daughters, 14 mo. old son, and new baby girl 3 weeks old.