I don't think people are understanding what I am saying, so I'm going to try and state it a little differently.
The reason that I say CR has to equal ECL (the only reason), is that the method provided for determing CR for classed npcs/monsters explicitly makes this assumption (in that it assumes CR = character level). If they are not equal (and the whole point of my starting this thread is that I can see they are not equal and I am trying to figure out how to deal with that with regard to high ECL races who are explicitly given a CR in one instance that is nowhere near their ECL based CR).
I can only assume that my explanatory abilities are sadly lacking, because out of all of the responses I have received, only a couple of people seem to understand what I am talking about.
To everyone else: I can appreciate, and probably even agree with your views, but they don't help me to solve my problem.
I believe that everywhere where I stated ECL = CR, I explained that I was stating this because it is a side effect of the level = CR statement in the DMG. I'm not saying I think it is balanced, or that I think it provides a solution. I think that if ECL is not supposed to equal CR, than character level shouldn't equal CR. If that's the case then I need a workaround for determing CR (or conversely ECL, whichever I choose to change) for high +ECL races (things aren't as bad with low ECL races).
I think as long as you allow monstrous races as PCs, you will always have to keep a list of abilities you don't want players to use, just like you would with magic items, spells, or anything non-core (and most DMs even have core stuff they don't use). There are balance issues with everything, but taking all of the monsters (who are, as pointed out by many, balanced for a single combat challenge) and allowing players access is just another balancing challenge for the DM. I believe the ECL system is not designed with combat balance in mind. It tries to balance a monster's abilities for the campaign, and the result is that it becomes unsuitable for calculating CR for combat scenarios. This is what I am seeking help with.
I am still evaluating UK's system for my needs, but I'm doing a fair bit of travel right now, so I don't have the luxury of sitting down with my books (and computer) and testing things.
Thank you to all who replied.