Oh hon, that is so scary! I've experienced that myself with DS2 and both DH and I were pretty much in tears. In our case it was coupled with slow weight gain and ended up being reflux. I don't know if the two automatically go hand in hand but you might want to ask your GP at your next visit, or make an appointment. Having said that, if he hasn't been diagnosed with it yet, you're probably in the clear.
I do wind DS2, though very gently. I just shift him from my arms onto my knee and that usually brings about a burp almost immediately, then I move him onto my shoulder to take him back to his crib and any remaining bubbles pop out then. You could also try rubbing a hand up the left side of his back, while he's on your shoulder. That's not jarring and usually gets the bubbles out.
What does he do when he wakes at 5:30? Is he happy chatting away in his crib or does he get agitated and start to cry and scream? If he's just lying there or chatting, I'd leave him until as close to 7am as possible, if he's getting upset, try to resettle him with Shh-Pat. Some babies are just early risers but sometimes you can teach them that wake up is at a more reasonable hour.
Seeing as you've been dealing with these for awhile I wonder if you're LO has low sleep needs? If that's the case, you could try pushing him for a longer A time to see if that helps. Try for 2.25 hrs and see if that helps? You'll need to give it a solid week before you see a difference.