Just a few side questions here...

What angle are your shelves on? And do they stick out beyond the air curtain formed by the front air disharge grille?

Flat shelves are easy to refrigerate, angled shelves will show up any shortcomings in air volume a lot quicker.

Is your rear air distribution duct fully perforated or are there holes cut at different levels for the individual shelves.

If you have done wholesale changes to fans and coil it sounds like an airflow prblem has occurred. Try measuring air velocities on an older non refurbished case and compare them to your new setup, I'll bet there is a difference in air volume that the fans are moving or static pressure developed by new fans is now less and can't overcome losses in air side pressure drop in new coil.