An EQ can helpful in dealing with room problems, but it isn't a magic cure-all - and no matter what else is happening, you will always be relying on the signal that is originally produced by the DSP, DAC's, and overall signal path (not to mention the amps).

The Yamaha that I had a number of years ago isn't a fair comparison to the 1400 you have now - it was a Pro Logic unit from around 1997. However, the move from a good Dolby Digital receiver to good separates will typically yield an improvement in sound. That's likely to be even more true if the receiver being replaced was powering the speakers. (Are you using the 1400 as a pre/pro only right now, or are the 1400's amps driving the speakers directly?) I've had my 990 for over a month now (seems like longer, but it's been a crazy month or two), and I am still extremely impressed with how it sounds.

The 990's channel trim and crossover settings are global, plus there is a global two-channel sub trim to reduce the sub's presence with stereo modes. AV sync is typically caused by video processing, so if your processing takes place downstream of the video monitor output from the receiver a global sync is fine - but if the problem is video processing in a source component such as a DVD player, line-doubler, or HD receiver, then you really need the AV sync to be independent for each source. Most folks don't need it, but if you run across a source that does need it you'll be real glad you have it.