I'm building a new home theater from scratch - all new components- including electronics, speakers and monitor. It seems like most of the newest devices are using HDMI- but from what I read about the 990- it uses DVI i/o, not HDMI. Am I missing something or does that mean I can't connect sources or outputs that use HDMI to the 990?

I've got a FAQ on HDMI in my sig that might be handy, but basically HDMI uses the same video format as DVI (since it borrowed the format from DVI) so that you can use HDMI-to-DVI adapters or cables to connect HDMI devices to DVI devices.

You cannot deliver HDMI audio signals to the 990. This is because when the 990 was developed, the standard at the time (version 1.1) was still very new and two revisions were known to be in the horizon. There was no way to assure any sort of upgrade path to support those future revisions or to know how v1.1 would fit into the marketplace. The only HDMI sources that really offer anything different over HDMI audio connections than over regular coaxial or optical digital audio connections are HD-DVD and Blu-ray, as my FAQ explains.