(1) You are correct. PLIIx is an extension of PLII that adds surround back channels. Where the Model 950 used Cirrus's Extra Surround to generate a mono surround back signal from 5.1 sources (including PLII, Dolby Digital 5.1, and DTS 5.1), the Model 990 will use PLIIx to generate discrete left and right surround back channel signals from 5.1 sources (again including PLII, DD 5.1, and DTS 5.1). If you have surround back speakers, this can be pretty cool. If you don't, you'll never use it.
(2) The 990 includes a few new surround modes: Pro Logic IIx, DTS 96/24, Dolby Virtual Speaker, and Dolby Headphone.
(3) HDMI's video format is borrowed from DVI. You can use HDMI-to-DVI and DVI-to-HDMI adapters to connect between HDMI and DVI components. This means that the 990's DVI switching will allow you to use DVI or HDMI sources and connect them to a DVI or HDMI display.
(4) A 5.1 system will not make use of some of the 990's processing modes (PLIIx, Dolby EX, and DTS ES), this is true. However, there's more to a processor than the surround modes. We still haven't gotten to hear one, and that will be perhaps the most telling test.