One other thing you might try. You tried to formally change the indentures but, as you found out, that's tough regardless of the issue.
If your HOA has a Grounds Committee or Landscaping Committee or something similar (some group of owners who can approve, let's say, color of shutters or front door, or design of a mailbox), you might approach that committee and ask for permission to build your fence. Now, technically, your rules don't allow for a 6' fence, but committees have been known to look past the rules in making their decisions. It's not a great way to go about it--your attempt to modify the actual rules was the right way--but recognizing that others have already done so, with the apparent acquiescence of the HOA and the appropriate committee--you might be able to receive approval for what you're seeking by using that technique.