Is it possible that you are just sore because you started riding again?

The bike size does not sound unreasonable but as you point out, there's more to fit than frame size.

For the knee soreness, focus on spinning to minimize strain. Try to maintain 80-100 rpm on the flats.

Back and neck soreness can be caused by lack of particular muscle group development and work itself out over time.

Try riding on flat pedals with cages if you have been using cleats to narrow the possibility of pedal issues.

Just some thoughts.