404 Problem

Hello Forum. I had an old website that I converted into a WP site however I couldnt transfer over alot of content that was indexed and now it showing up in Google Keyword Tool as broken links. I installed 404 to start and google just crawled those pages again and csme up with alot of 404 errors. When I go to Google and click the links they go to my home page like I choose. Is there something I can do on the WP end to make those 404s not show up as broken links?

Thanks in Advance

Mike