wheel upgrades on a budget

One cost effective way is to get a wheel cover for your rear wheel.  You end up with a disc wheel for about a $100.  Here's a link to their website: http://www.wheelbuilder.com/store/product.php?productid=16265&cat=284&page=1  Then you only need a more aero front wheel.

Another site to check out is http://www.neuvationcycling.com/wheels.html  They've gotten some good reviews.

Not trying to beat a dead horse with another discussion on cost vs areo advantage but you might be better off spending money on an aerohelmet and get more bang for the buck. 

Ernie

I just upgraded to a set of neuvation wheels. Best bang for the buck by far. http://www.neuvationcycling.com/

For improving bike speed, aero bars & time-trial helmet are WAY more important than wheels. Check out this well-done est:

http://www.cyclingnews.com/tech.php?id=tech/2008/features/jeffs_need_for_speed08 

Starting with a fast road bike & competitive cyclist, energy savings at 40kph (25mph) were- 

clip-on aerobars- 30Watts

Time Trial helmet-  10Watts

Full TT bike with full aerobar & HED 3 wheels- 20Watts (est 9-10W due to wheels)

Your Nemesis is a TT bike, so you already have the aerobars.   TT helmet is relatively cheap speed. Then work on your best position- most aero while still (relatively) comfortable.  Best wheels help a bit, but it's expensive.  

For $400, doubt you'll get significantly faster wheels unless you find a killer deal used.   Look at any used wheelset VERY carefully before you buy (check rims for small cracks/crash damage/excess wear, hubs for smoothness/proper adjustment, spokes, etc.).  Fixing high-end wheels can get into big $$$$.