Hey everyone! I'm a pretty active bumpie over in the March14 board, but this is my first time here

My LO was born on March 23, and he's now just over 4 weeks old. We tried exclusively breastfeeding first, but he had trouble latching and he developed jaundice soon after he was born, so his doctor had me supplement his feeding with formula.
Unfortunately, this led to bottle feeding, which led to latch issues, which led to pumping and supplementing rather than breastfeeding like I wanted. After meeting with a lactation consultant last week, she told me I could still breastfeed even though he had been bottle feeding for 3 weeks.
We've been trying and he latches on to my right breast pretty good, but it makes my nipple/breast hurt during and after he finishes for a while. Is this bc he's latching incorrectly, or is my breast just getting used to breastfeeding?
My left breast has a flat nipple, so it's harder for him to latch on. When feeding from the left he pulls off quickly and screams and flails. I don't know if this is a let down issue, or the flat nipple, or flow confusion from bottle feeding.
I should also mention my AF started after just 3 and half weeks. Does this change things? I've noticed my supply on the pump drastically reduced around the time I started AF. I went from pumping 3-4 ounces per sitting to barely 1.5 ounces.
Breastfeeding was already overwhelming, but even more so since we've had a rocky start. Is there anyone else out there who breastfed after their baby was established on the bottle? Advice is welcome!
Edit: forgot to mention something.
Re: Looking for Advice/Encourgement
Good luck with your LO!