Both my girls were breastfed, formula fed, then transitioned to cold milk just fine, so don't worry too much about it.
For the first, we transitioned over the course of about ten days using the bottle. We started with room temp formula as well, then moved to 1/4 cold milk + 3/4 room temp formula, then changed the ratio every couple of days. We never warmed the milk up, and since each bottle was just a mite bit cooler than the ratio before it, it was a good gradual transition. By the time we were at 14 months, we had switched over to sippy cups entirely.
For my second (who is just turning two next month), we would give her a sippy cup of 100% milk at the table with her meal, then over a week, we did less and less formula in bottles and then just dropped the bottles entirely. She was wanting to be like big sis anyways, so switched to sippy cups easily.
Both ways worked fine.
We did switch to organic milk (not everything, just the milk) about 2 years ago. Mostly because we have two girls and we were hearing about possible links between the early onset of puberty (menarche) and growth hormones being given to cows coming through the milk. I don't know if it is true, the science on that is probably still several years away, but with two girls, we decided it can't hurt, and might help.
Not sure if I'd worry about anything similar with a boy, but talk to your pediatrician to see if it would be worth it.
Good luck!