Very interesting way of thinking about things. It's very fun to discuss such stuff with people that have thought about this to the level you have.
"If you reject this set of desires for some reason,
then you are immediately confronted with the
problem of what to replace them with, what
goal and motivational structure would be better?
This is probably the most profound question of all."
Yes, very fundamental questions.
Evidently your base desires aren't too bad, enough to think you may not want to change them, once you are free to do so, which is good. But some people have baser desires that are very bad. For example, some people are masochistic. In that God/Evolution, hard wired them to want to hurt other people. Thankfully, most people have this under control, but obviously occasionally, peoples wiring gets effed up, and they go postal, and so on.
Obviously, those types of people don't really want to want, what god/evolution wired them to want, so surely they'll want to change themselves to want something better than that.
As far as what might we want to do, other than base desires, for starters, there is plenty to keep us busy. In fact, we've started a [http://canonizer.com/topic.asp/120 survey topic to prioritize things] to 'canonize' just such a prioritized list.
It includes things like finding out what everyone wants, first. It includes things like achieving an ability to understand the mind, so we can 'upload' and change things like what we want. This is very high on the priority, because it solves most other problems, like solving the problem of people that want to hurt other people, and so on. It solves the problem of death. And most everything else.
Then, once we do all of those kinds of things, for ourselves, we need to solve the problems of everyone that is less than us. And this, of course, includes people that didn't make it to the millennium. In other words, we've got to work on resurrecting our ancestors, to pay them back for being our creator, and doing all the work to create what the immortals freely inherited.
I'm betting doing all of that, for everyone, is all going to take way more than 1000 years. And once we get all that done I bet we'll know what we want to want, as you also indicated, right? Surely, at least exploring the rest of this huge universe, resurrecting any alien life forms that didn't or haven't yet made it, and so on, will be high on any list.
"Hey, Robot, get out of the way, it's my turn to take out the garbage!!!"