Hi there, welcome to BW.
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I guess I need to start off by asking a few questions. Is he medicated for reflux? Often times reflux babies wake to feed in the night to soothe the pain. Does he sleep on an incline, use a paci, any of those things that naturally help reflux? This really sounds like it could be the case for him feeding so frequently.
How do you know you have a low milk supply? If that's truly the case, then I would be feeding him on both sides during the day and at night to increase your supply. Both my kids started feeding on two sides right around 3-4 mo.
Would you mind posting your full day EASY for us to have a look at? From just what you've posted in the evening, it looks like he's most likely going to bed a bit overtired and I'm guessing that's the reason for the initial wake at 9 pm, not hunger. I also don't think you need to feed him twice in the hour before bed, but let's see what the rest of your day looks like before we make big changes there.
Does he not last 3 hr between feeds because he has short naps, or do you think he's going through a growth spurt (there are many during those first few months)? I would really work hard at getting him to take full feeds and getting to a good 3 hr EASY. If you need to feed more frequently for a few days to up your supply, then do it, but I definitely think the snacking is hindering far more than helping here.
Finally, 45 min naps are pretty common at this stage in the game, as they are often developmental. If you are getting one good long nap per day right now, that's just fine. Although, you're bound to get great help on the naps forum as well.
Hope that helps a little, will wait to hear back from you.