The highly efficient Klipsches are the reason for your high levels - 97dB is a long way from the typical 86dB to 92dB efficiency most speakers offer. In cases like that, it is often best to do something along the lines of what you are doing - move the master volume down to -10dB or -20dB, then calibrate to 75dB there (with the settings you ended up with, I'd probably go around -10dB so that your adjustments ranged from -5dB to +5dB).

I'm not sure about the "jumble" you are running into. The first step is probably to get all of the channels well adjusted (the sub will likely need a fair bit of further tweaking as you listen to stuff - think of it as "seasoning to taste"). After that, try some familiar material and be aware of the processing being applied - CD's or DD 2.0 DVD's that you have been listening to in stereo may sound a lot different if you let the 990 default to surround. Let us know how it goes...