It's not just that the bike could be small, it could be the frame geometry.

I concur that rising your handle bars, and bringing them back towards you could make a difference. You raised it, but did you use a shorter reach stem, and you can use a double stem to bring the handle bars back towards you more.

Bikes have to fit, and it's not just about you standing there over the bike, or riding it a mile.

With me it was always reach, and leaning. I road around on a colorful Bianchi Eros for 4 years. I need a 56 CM in a vintage bike, and it was a 48 and never gave me neck pain. I found it comfortable to ride. No knee pain either.

I have had vintage 56 CM roadies that killed my neck, a beautiful Trek 660 comes to mind. It fit well, but because it had a long reach it bothered my neck badly.

It's why I don't like putting down money on a bike without a decent return policy. I have never purchased a new bike, but I will be buying from a place with such a return policy. (I am not saying the OP bought one way, or another)