If your convictions were vacated and expunged, then you should not have a problem getting the CPL reinstated. The requirements for getting a CPL are lengthy, but I am assuming that you were only suspended because of the charges:
The laws regarding prohibition on a CPL or even for possessing a gun only apply when you have certain kinds of convictions. But once the convictions are vacated, they no longer exist legally, so they no longer operate as a bar to your getting your CPL.
I'm sorry you are getting the run around from the county clerk but they should be reinstating your license:
"If a county clerk suspended a license under this subsection and the individual is acquitted of the charge or the charge is dismissed, the individual shall notify the county clerk who shall automatically reinstate the license if the license is not expired and the individual is otherwise qualified to receive a license to carry a concealed pistol, as verified by the department of state police. A county clerk shall not charge a fee for the reinstatement of a license under this subsection."
You should be able to show them the paperwork stating that the charge was dismissed to get it reinstated.
Hope this helps.