Volume settings are tied to the reference level calibrated to - it's possible that the 635 was intended for an 85dB reference level instead of the 75dB level used by the 990's test tones (and many calibration discs). You could raise all the channel trim levels an equal amount, but unless you are operating regularly at 0dB or even +1dB or above I wouldn't worry with it.

The DVD player's distance settings, channel trim settings, and bass management only apply for the multichannel analog output. Because of the 990's ability to apply bass management to the 7.1 Direct input, I would recommend leaving all distance settings and channel trims at zero and set all speakers to large (and sub to "on").