Replacing the stock speakers and feeding proper power to the system are the best things you can do for the sound in any car stereo, bar none. Keep the original head unit if you must, simple kits can be had to convert the signal going to your amp. Pricing is useless, however, because installs vary wildly in quality, and component cost varies quite a bit as well, depending on if you pay retail or not, and how high end your components are.
If I had to guess I'd say labor to replace the stock door and rear deck speakers with similar size components could vary anywhere from $150-600, not including mounting and wiring up a new amp. Installing a new head unit (barring power issues) generally runs from $50-100. I think I once paid $900 for door and rear deck speakers plus a new head unit in a Maxima I once owned at a really high end shop, with decent speakers (not top of the line though), dynamat, the works. Worth every penny.
Hardware is a whole different issue. Speakers can run from $50 for the whole set up to over $600 for the front speakers alone. Wiring can range from $25 worth of cheap zip cord and patch cable to a couple hundred for high end wiring harness with quality braided wire, plated interconnects, etc. If you get serious enough to add a sub, you're could be looking at a custom, built-in enclosure, or a cheap pre-fab box bolted to the deck. Amps can run from under $100 to over a thousand.
I'd suggest going to your local best buy, getting an estimate for a basic consumer-grade system and install, and then going to your local high-end auto sound specialty shop, finding out the price differential and then deciding what you can live with.
For the record, I'm thrilled with my setup. but it wasn't cheap, nor is it finished. :-D
http://www.kalani.net/Car/Lexus.html
-KMan