Hi
My third child is 16 months now. Still being on a bottle isn't all bad just before one year. I know with my first two we took the bottle away right at one year; with our third it went a few weeks later.
Some things that might be worth trying is:
1. Instead of sippy cups, try cups with flip up straws (that's all my daughter will use).
2. Try rotating your evening routine so that the bottle is first- while he's still toddling around- long before the actual bedtime routine starts. Maybe you can gradually take it out of his bedtime expectations.
3. Try watering down the formula litlle-by-little or switching to whole milk. Maybe this will start detaching him from this dependancy.
Lastly, I know it's hard but sometimes it's ok to let them cry. It usually will abate in a few days.
Oh, in address to his naps: don't stress that too bad. Usually just around or past a year, their naps will start to draw to a natural flow. of just once a day at the right time. Plus, I used to work alternating shifts with my husband to avoid daycare. Because of it, the person coming off of nights often needed a nap. Maybe this is why your little one is napping in the morning. If it works for y'all (and you don't have to worry about childcare center needs) then I don't see a problem. Often as parents we're too busy thinking our kids, routines, development, etc, has to measure up to everyone else. It doesn't. You're doing great with your son!