Hi there, welcome! The 3/4 month mark is really tricky for sleep. Let's see if we can sort out what's going on here.
I have to work really hard on his naps, he usually will nap for 1hr or 1hr 15 minutes...sometimes it may only be 45 minutes but I usually have good success in getting him back to sleep at these times for another 15 to 20 minutes.
Even though he has a hard time staying awake for more than an hour during the day, this really makes me think that he can use some more A time. You can stretch it quite slowly, just by 5-10 minutes every few days. I found with mine that we had to do some moving about the house to keep from getting too fussy -- and we'd generally just end up in his room towards the end playing quietly on the floor. Better naps will help your nights as he won't be quite as OT at bed time.
I recently began exclusively bottle feeding - before this was doing a combination.
Did your increase in wakings coincide at all with this? It could be that you need a different flow nipple/teat on your bottle or that he's a little sensitive to the particular formula that you're using. If there's some connection, I'll find someone who knows much more about bottle feeding than I do to do some trouble shooting and see if there's something that needs to be tweaked there.
This first time around 12:00 where he'll finish 4 ounces (but he seems like he could probably do another 1 or 2)
Just out of curiosity, why don't you give him more if you think he could take more? A 13 week old baby definitely needs to eat at night, it's really just a whole lot of luck if you manage to get away with not feeding them at night at that age.
I'm wondering if the paci is the issue here? As he seems to generally settle quickly with it.
It very well might be -- he seems like he's having trouble transitioning between sleep cycles without it. He's way too young to learn to replug -- none of mine ever took the thing, but I think the conventional wisdom at this age is to either deal with replugging it yourself, ditch it completely, or take it out before he falls into deep sleep so he's not looking for it when he goes into lighter sleep.
Is he falling asleep independently at bed time?