3 Month-old growing pains

So, Ezra. He is adorable, smiley, kind of goofy....and driving me crazy between the hours of 7-9 pm. We were doing great for a while. My good friend, and Public Health Nurse, Frances suggested swaddling at the 4 week mark when he would cry for an hour at 9pm. Once he got a bit bigger, and wigglier, we stopped that. Then came the suggestion that he was going to bed too late, so we started his routine at 6:30 to have him in bed by 7:30. For weeks it worked. I gave him a bath, read him a story, nursed him and put him in his crib almost asleep. There was a night that I actually didn't hear from him for 7 hours!
Now, he cries. He cries and he cries and he cries. I put him in his crib sleepy, within 20 minutes he cries. I give him his soother, he cries, I swaddle him, he cries. He is now not going to sleep for the night until 9 or 9:30- even though he is in bed by 7:30. He cries, on and off, for almost 2 hours.
I really hope this is just a phase or a milestone or a something...