Well if you are going to do this remember there is going to be:
Are you really going to want to run all the wires for all of that through the car? Sounds like a lot of unnecessary work to me. What is wrong with the harness now or what did they to do it and why?
If you do replace the speakers and use the stock amps you are going to need to do research on this because you don't want speakers that have the built in tweeters also you are going to want to look for a high ohm (I think it is the high ohm ones I cant remember) speaker to use with the mach 460.
Its all going to depend on what you want out of your system some just slap in any old speaker and hope it sounds good, and others go all out and make sure that it will all work together. A good place to call and talk with would be crutchfield they will talk with you and give you some advice they are very knowledgeable about things like this and do it everyday.
You can do this though and it will sound great with a little work up front it will save you headaches down the road! Good luck!