Hugs - Its tough when things go from good to not so great.
How are you feeding? If BFing - wondering if you have a fast letdown:
http://kellymom.com/bf/got-milk/supply-worries/fast-letdown/? This actually can cause lots of issues with sleep and leaves a lot of gas trapped in LO's gut and is quite painful. DS had terrible gas from my fast letdown and would often root for a feed an hour or two after a feed because sucking will start up the reflex that pushes everything along the gut and relieves the gas the most painless way possible. I had to pump DS' legs and keep feeds at least 3hr apart for a day or two. Also lying back to feed helped to reduce the flow a little because it was going against gravity:
http://www.biologicalnurturing.com/If he's mainly struggling with gas after that 3/4am feed, that could be that you're engorged as that's in the middle of the prime milk-making time for your body.
How long is he awake before a nap? Is there any way that works to get him to nap longer, like does he sleep for longer than 45min if he's lying beside you or on you? What about a pram/carrier? You may have to do whatever you have to, to keep him well rested for the next few days - if he gets too overtired, he will wake from that as well as the gas.