I happened across this thread, and am sad to hear about the lack of service this company is capable of offering since I recently purchased an onkyo 876.
One thing I remember reading about the integra 9.8 is that to bring it to market at such a low price, they had to make some trade offs, and one such was the components that handle analog audio. I hadn't heard if the 9.9, being more expensive, included improvements in this area, but that might be a plus in it's favour.
Dave, I know this wait must be really a bad experience for you(I had a projector that needed warranty service - in JAPAN!), but if I had the chance to upgrade for $200, I would have jumped at it. I think the store you are dealing with is actually giving you a decent offer for the following reasons.
The 9.8 has been replaced by the 9.9 as you know, and they are obviously having a hard time securing one for you. Also, the 9.8 had some issues that would have been addressed in the 9.9(bitstream bomb, audio switching/lipsync delays). That's why I got the onkyo 876, because I knew Onkyo/Integra don't have the best service, and the 875 had possible issues.
If I were you, I'd go to the dealer you're dealing with, and say you'd be willing to get the 9.9 for $200 if they promise a no hassle exchange for another 9.9 should you encounter any problems.
You've been beyond patient, and I know Integra's name is mud at this point, but this may be the best option besides waiting another month or two.