I would switch back to the formula 2 right away if it was me. It sounds like something in the formula 3 just doesn't suit him.
I actually have no idea what formula 2 or formula 3 are but I'm guessing it's marketed as a more grown up drink. The advice in the UK is that there is no need for any formula other than "first" the one which can be used for new borns (by 'no need for any other' I do not mean those for babies who have allergies, obviously they are needed). Here 'follow on' formula is marketed, this is because they are not allowed to advertise or do price offers on "first" formula as this might discourage BF. Really marketing is the only reason why these follow on formulas exist. I don't know about where you live, just saying how it is here. My guess is that formula 3 does not have additional benefit which would be lacking in formula 2 so just stick with what is taken well and doesn't cause problems.
Personally I would want to keep at least one of the milk feeds to a relatively good amount. It is not strictly necessary as calcium, fats etc can be found in other foods but in general milk is good for them. For that reason if it was me I'd keep going with the bottle until I found a way for the milk to be taken in a good portion. Will he take the larger portion of formula with a straw? If so I'd do that.
WRT switching from formula to cows milk maybe you can do that as a separate step (either before or after switching bottle to straw)? Have you tried a gradual change over by switching 10-30 ml of formula with cows milk and shake to mix. Then after a few days switch another 30ml and so on, keeping the intake good but gradually he gets used to the different taste?
When I switched the BT bottle to a drink of milk in a cup and a solids snack I kept the morning bottle so it wasn't so important the BT milk reduced in quantity as he was getting his main milk drink at another time. I did the BT supper with drink of milk in a cup around 1.5hrs before sleep, not later than 1hr before sleep.
I used to avoid fruit because I felt like it was too acidic for my DS before bed, usually I gave carbsy type things such as bread, toast or pancakes (which did contain fruit but it was cooked in rather than fresh fruit), crumpet, bread sticks. I made no added sugar mini muffins which were good for supper with milk too.