To which I say to your legal counsel respectfully, 'bologna!'
Go back to the first post in this thread.
The HUD RESPA FAQs Charges that the seller pays as a matter of common practice and experience are not included on the GFE."
If they're not included on the GFE, how can they be part of the tolerance comparison? What is your legal counsel basing his opinion on?
As to your software being wrong, more than one attorney probably weighed in on that not to mention how all the software providers held off and really worked to get it right. The only errors I've found on software, especially this late in the game, have been minor.
Sorry but I think you're getting some bad advice. I know how had it is to fight that too. I'm going to go dig a bit more in the FAQs and see if I can find some more supporting documentation for you.