You can get improvements in a couple different direction.  You could put togehter a 2.1. system that stands alone or you could upgrade your existing hardware and or speakers. 

There is so much you can do to upgrade the curent system it is tough to know where to start.  What are you least happy with? 

You have fewer options for a 2.1 system.  that will be easier to suggest but would prefer to know which way you are leaning. 

To maintain the integrity of your video playback in 5.1 you are probably going to want to get three speakers if you upgrade your existing system.  In video, integration of the Center and Fronts is critical.  Magneplan is an extraordinary value and you should be able to get fronts and a center from them for ~$1000.  Beauty is they have a 60 day return policy so if you don't like them or they don't give you the improvement in sound you are looking for you could return them.  Emotiva is another great company that delivers a value.  B&W's 600 series will have 2 bookshelf speakers and a center channel for about ~$1000. Def Tech and a variety of other companies will have options.  You will likely get more speaker from Magneplan or from Emotiva and have the in home demo.   

You would be hard pressed to get a separate pre-amp, power-amp, DAC and speakers for about $1000.  You could get all those parts from Emotiva excluding speakers for about $900 and speakers will likely cost you about $500 at minimum.  . 

A alternate solution would be an integrated amp with a DAC.  Right now Needledoctor has a Cambridge Audio Integrated on clearance for $299.  Emotiva has a great DAC for $199.  You could get the NAD DAC 1 for about $299 and Cambridge has a great DAC for $359.  Depending on which one you choose your could have $500 to spend on speakers.  The Mirage Omni S8 is a great musical sub at about $250.  For speakers, Infinity Primus 153 would keep you slightly under budget at $218, 163s would put you a touch over budget at $278 and  Emotiva XRM4.1's would put you about $100 over budget at $340.  I think that would be a pretty great sounding system for ~$1000 to $1250. 

The only thing that wouldn't be returnable would be the integrated AMP as it is a closeout.  Everything else can be had from Emotiva and Crutchfield who both have 30 day return policies. 

Good luck and I would love to hear what you end up settling on. 

I made suggestions on the speakers based on pice point, value and returnability if you don't like them.  The only thing I can say is when I bought speakers I listened to pobably 50 different lines in my price point to settle on 2 that I really liked.  Speakers are extremely personal and what I like may not be what you like so spend your time searching here.  Again, the nice thing about the speakers above is that they all can be returned if you don't like them.