I wouldn't bother with toddler formula if he is going ok with cows milk. It's up to you of course though. He probably doesn't need the lunchtime bottle anymore, if he is not drinking much of it and it sounds like he is getting enough calcium from other food anyway.

Just keep persevering with the cup, he will get the hang of it eventually. I would try giving him cows milk or a milk/formula mix in his morning and night time bottles and see how he goes with that. If he takes to that then you can phase out the formula.