I want to be able to find all the D Drop C songs, but there are a number of them categorized under Other because they were created as CGCFBE, for example. I would like to change these all together, otherwise, every time I hit save it scans everything again!

In the folder where CFSM is installed (presumably C:\Program Files (x86)\CustomsForgeSongManager), there's a file called RocksmithToolkitLib.TuningDefinition.xml. 

You can modify it by adding a new tuning definition for the this tuning (or any other you may need) and if it matches, it won't show as Other any more.  
Just follow the existing format,

<TuningDefinition Version="RS2014" Name="CACGCE" UIName="CACGCE" Custom="true">
    <Tuning string0="-4" string1="0" string2="-2" string3="0" string4="1" string5="0"/>
  </TuningDefinition>

and modify it as you see fit.  (I'd assume since it's BE, string4 will be equal "-5" and string5 to "0")

That wont fix the songs that have the incorrect tuning? That will just add a tuning

I think the songs were originally created as 4 string tunings, with the last 2 strings defaulting to BE

If I have 10 songs that have the CGCFBE and I want to update them to D Drop C, I have to go into each song file update then wait for the rescan, that takes forever!