Thanks for the input everyone! We had another rough night last night. It's the third time since we started milk (a week+ ago). He woke around 1:30am. I thought I was going to have to go in to help him back to sleep, but after about 10 min of crying he settled down on his own (I was in the middle of preparing a bottle when I heard him going back to sleep). I haven't cut out the milk yet since I thought it was unlikely to be the culprit. Now I'm reconsidering...
The formula we've been using is Gerber Good Start Gentle. I've always thought that he has somewhat sensitive digestion and we tried a bunch of different formulas before settling on Gerber (he was EBF until about 4 months, then a mix of BF and formula until 10 mo, then FF only). Right now I'm giving him bottles that around about 1/3 milk to 2/3 formula.
He's had a bit of a rash develop over the past couple days along his back where the top of his diaper rubs on his back. It looks like heat rash to me, little raised red bumps, and I figured his skin just got irritated from rubbing on the diaper. Could it actually be from the milk?

I've been trying to look at his teeth/gums but he doesn't like to let me look. I think I see one of his upper canines working it's way out, but it's hard to tell. He's been gumming on everything recently, so it certainly could be teething.
He is really working on standing/walking right now, so it could be that waking him up. I try to give him lots of time to practice during the day.
It's so hard to know what's going on when so much is changing with him all the time! I just wish I knew how to best help him.