Minecraft – How to disable commands for only 1 or 2 opped players (like worldedit and vanish)

From your description it seems that you have done it in exactly the opposite order. (It would help if you also posted your script, though.)

When you 'inherit', it means the 'child' will inherit all of the parent's members and can also add its own. So basically what you did was, you let anybody (even default) use everything it inherited from every group all the way up to owner.
So basically what you need to do is:

1. define the default group
2. define member and set its parent (i.e. let it inherit from) default
3. let moderator inherit from member
4. and so on.

That should be it.

Edit: Yesterday at night I was pretty tired, about to go to sleep and a bit worried whether what I wrote would make any sense in the morning. Luckily it doesn't look that bad; so I'll even add an example now. :)

Make your yml file like this:

groups:
  Guest:
    default: true
    permissions:
    - modifyworld.*

  Member:
    default: false
    inheritance:
    - Guest
    permissions:
    ...etc

(I've named the default group Guest for clarity.)

FTB does not, as of the time of writing, support Bukkit. If you want to maintain Bukkit functionality and the ability to use plugins, you should follow SevenSidedDie's suggestion and rebuild FTB from the ground up on MCPC. You can find information on the contents of the various FTB packs here.