I am currently working on a similar project- moving our company intranet to sharepoint.
If you want to use web parts- your going to have to re-do the whole site in sharepoint. WHat I'd suggest- for your background information is to visit
http://www.msd2d.com and go to the webcasts area- they just finished up (but they have them archived) a series on sharepoint that is very informative for the new user to Sharepoint 2003.
There is two books out at the moment on sharepoint- neither from Wrox. I think they have one in proccess. (I wish I was part of that Tech Review team... I'd love to get a peek at the book). But in any case, I'd look at MSD2D first for that information. There are some things thay don't cover, and I think are critical..
I should write to Jim and see if he can make a sharepoint forum. I'll do that now.
Hal Levy
Web Developer, PDI Inc.
NOT a Wiley/Wrox Employee