First off, as a student in a similar postion, I can offer one piece of crucial advice: you need to make sure you don't go back to grad school. It's really killing my system.

Basics here, as I'm sure there are lots of people more qualified than me to address some of the issues you raise. There are a few tradeoffs you are going to have to make given the budget, but these may work given your listening space. If you're comfortable doing it, I'd recommend sacrificing some bass to get better sound--it's always a challenge convincing the 20-something crowd that your system is worth the price if things don't fall off bookcases, so it's not an easy tradeoff to make but the benefits can be huge. If you're willing to go for bookshelf speakers, you can really get some excellent imaging for a reasonable amount--it's also much easier to move which is a concern (the day I moved my magnepans into a 3rd floor walkup was tiring, and about as stressful as a pregnancy scare). If you really want to add bass, you can do a subwoofer later in the game, which isn't that bad of a call either, as musical subwoofers are becoming less rare, and less expensive with time.

Also keep in mind that you are probably going to be in a small room for a while, so having a 5 million watt amp isn't really that imporant (especially if it's driving bookshelves). As far as DACs go, there are a lot of options, at a lot of prices, and they do seem, to me at least, to get noticably better as you spend noticably more. You should listen to a lot of them, see what strikes you as the most musical and pleasing, and try to ignore stats, as this is where digital meets analog, as in analog that gets to your ears. The ears are the intended audience, so they make a good judge.

Specific recommendations:
I'm currently using B&W 601 S3s in my main system, I recommend giving them a listen, they won't blow you away, but they have pretty impressive imaging for the price (I think it's about $400), and offer enough bass that you can get away without a subwoofer with most recordings. I'd also look at the high end bookshelves from paradigm and PSB (closer to $1000), both sounded pretty buttery to me. If you want more bass, I had the last version of the psb image series floorstanders, and can confirm they have pretty decent range and are pretty musical--though less so than my current bookshelves, and much less so than really high end bookshelves. Imaging was kinda iffy--which probably had as much to do with placement as the speakers, but plenty of bass for music purposes. Placement is going to affect imaging a lot, so it's really worth your time to home demo what you can--if the imaging sounds $500 better at the dealer, but is indistinguishable at home, it's probably not the best use of your budget at the moment.

Solid state amps have been around for a long time, and you can get huge bang for the buck here. If you're going to scrimp at any phase, this is where I'd do it. You can pick up a good rotel or parasound 2-channel amp for $400, and your major limitations will be your sources and your neighbors. I had a 30 watt rotel integrated driving mangepans in a 25x14 room (not recommended) with pretty solid results for 6 months. So to summarize, a low power high current solid state amp should do a lot of good for your sound and budget.

So all you need now is a DAC (right? it sounds like you have pretty decent volume control on your source, so you can skip a preamp for now--if you need volume control, listen to the rotel integrateds, they start pretty cheap and don't sound it). Don't know what to tell you here, I'm still researching how best to do this on a budget. There seem to be a lot of used ones around that aren't that pricey, but you can't listen to them. I can confirm that a $4000 meridian sounds great, but that's probably as useful to you as it is to me.

Cables? Deal with that when you have some idea what you're spending on components. Spend more than $5, but in a $2k system, I'm not sure how best to budget for that.

Good luck, happy hunting, and again, sorry about the addiction.