I disagree with Monster's recommendation to switch the pre-amp, but that's just me. (Plus, I know my wife would flat-out never go for having to walk up to the power conditioner to turn the system on, and I wouldn't really care for it myself - there are reasons I've invested some time and money in a good universal remote, and putting a physical switch upstream of the system like that runs counter to those reasons.) They may have some reasoning for the recommendation, but I don't see it - especially since they didn't include any sort of trigger inputs on the 3500 (at least not from the pics I found of it). The current draw in standby is going to be tiny.

If the amp is delayed a few seconds after the Monster is turned on but the pre-amp doesn't come out of standby immediately, I see no benefit to the delay - the amp is at that point on when the pre-amp wakes up. Personally, I'd use a trigger cable to turn the amp on and off from the 990 and leave the Monster on all the time. You lose the delay, but I don't see that you're getting a benefit from the delay now anyway and there are plenty of folks with installations this way that suffer no ill effects.

As for the new buzz you are getting at start-up, I can't explain it. I'd probably start by checking my wiring, particularly power cords near the amp's inputs. Another interesting experiment would be to turn the amp off at the front panel, turn the power conditioner on, and then turn the amp on just to see what happens.