the counter in the 2000GTL is made to compensate for the SSB offset and won't display the change. (if that is what you meant by your last post)
the C945 is a transistor and is probably just fine. i would leave the clarifier mod in if the radio is working. do all the steps i list here and then change the clarifier mod if desired.
If the radio was here in my shop, step one would be to clean the junk out of it with some chip brushes and then clean all the pots and switches with contact cleaner.
then i would remove all that brown glue that is all over the place, as it is corrosive and becomes conductive over time (guaranteed it is already starting in your radio).
you need to unsolder the parts from the board and clean them completely. there are videos on youtube on how to do this as well as what to use as a solvent for the glue.
DO NOT just scrape and pick at it!
after that, replace ALL the electrolytic capacitors with brand new ones. this includes the caps in the freq counter module. be careful here as this board is double sided and plated through, meaning that you have to get ALL the solder out before trying to remove the part. failure to do this right results in pulling the sleeve out of the board.
you can buy cap kits on ebay from klondike mike. (my opinion is to avoid the other cap kit sellers out there)
once all that is done, then do an alignment on the radio. you need to get all the basics done before you troubleshoot an old radio like that.
If all went well, i would then remove that cap and coil and see what change it made, and whether or not it needed to be in there. (my guess is that it doesn't)
there is no point in trying to fix a radio that has caps that old in it. you will only be chasing your tail.
LC