Hi
Most of the routines I've seen (including ours) there's a mid morning snack, which you don't appear to have/need. So
milk
breakfast
snack
lunch
snack
dinner
milk
But, if she's taking a good lunch at 12 then there's no reason to change it. Perhaps just switch the 2pm bottle to a snack like you said.
WRT switching to cows milk. If your LO doesn't take issue with the switch and hasn't shown any allergies you can just switch. My DS didn't bat an eye when I changed his formula to cow milk. If she refuses it you could switch an oz at a time so that she becomes gradually accustomed to the taste.
WRT the BT bottle and teeth brushing. I would totally recommend brushing teeth after the bottle. Although milk isn't as bad as some drinks/foods it will still effect her teeth. In fact it was the whole brushing teeth after the BT bottle that motivated me to drop the BT bottle altogether. It was a very cosy part of our WD for BT and I didn't want to mess with our routine or wreck his WD and not having him sleep but I also didn't want cavities. I decided if I was going to alter the routine to put brushing teeth after the milk I might as well just get rid of the bottle.
In this thread I give detail of a totally pain free (and quick) gradual wean from the BT bottle, it's an option:
morning bottle still needed?(the details are in reply #14) The OP on that thread is 6 days in and already dropped half the bottle without any disruption to the BT routine.
FWIW I dropped the BT bottle at 12 months and the morning bottle at 13 months. The morning milk was switched to a straw rather than a sippy cup. LO can get a lot more through a straw (we use a wide one with the bendy bit - after use wash and save for craft projects if you like to recycle) and it can be an easier switch whilst still maintaining the milk intake which of course is still important.
hope this helps. There are no hard and fast rules, just various experiences.