When I say "Core" I mean things from the core package, like the Fighter or Druid classes. Those you can directly copy, modify, and then save.
Things from other packages, like the Magus class from UM, can be copied but cannot be saved (this is to protect us from a user just making a copy and easily distributing it to those without the package). For things like that, you can still sort of copy it, just not easily. You'd basically be using the unsavable copy as a template, and building a new class which mimics it.
Replacements are pretty simple to use, make a note of the original's unique ID (for example, the unique ID of the dodge feat is "fDodge"), create your new version (call it "fDodge2"), and put the old one's unique ID in the Replaces Thing ID field. That way anything in the system which would normally affect the old dodge is redirected to your new dodge feat, and the old one is not selectable any longer.
To be honest the exact number of classes to be edited is unknown however It could be expected to have minor changes to all classes (mostly feats they access that have been changed/removed/added).
The only ones that will have other changes are ones as mentioned that would have a class ability that emulates a removed feat.
I have done the tutorial for a very basic on adding abilities, changing spells, etc. I do not see spellcasting as being altered mechanically in the classes.
Spellcasting should be handled in the latter tutorials, which go through making the alchemist class.
So far it seems like I can add feats as class abilities using the Editor.
However, I am very green at this and any advice on efficiency is appropriated.
Is the idea that the feats are going to be completely unavailable to anyone who does not have the class which has an ability that emulates them? Because if not, why not just have the new classes bootstrap the feats that they grant? That'd be more efficient than creating new class abilities, surely.
Also is the editor capable of making a set of "house rules" in regards to a check box similar to how one would select a portfolio to use "Pathfinder Society" rules?
The very last couple buttons on every editor tab include the "Sources" button, which you can use to set up a "ddufour's house rules" source. One thing to keep in mind is that replacements happen regardless of whether any particular source is active. For example, if you make a new Fighter class, give it the house rules source, and have it replace the old Fighter class, there will be no fighter class shown when you don't have your house rules source enabled.