Redirecting pages listed within Google

[Ride45]

Hi,
We had 2 websites (We'll call them site A and site B) and we recently merged them into 1 website (Site A). Each site had 300+ pages indexed with Google, so combined, Site A is now 600 odd pages (each of which are UNIQUE and HTML driven).

For Site B that we took down, we pointed the domain to Site A and we put a custom 404 not found page for anything relating to that domain in the Site A directory. (Search for anything relating Site B, and Google results will link to a 404 page, customized, and which appears in the Site A directory - with site B's domain now pointint to Site A only - no files exist in a Site B directory)

Q: What is the impact of doing this on search engines. We don't want to lose potential visitors from the indexed listings, but we also don't want to try and trick a search engine in thinking there is an actual page there. Besides in the new Site A, those pages now exist.

What is the impact of this: with a bit of coding we could add functionality to a 404 page:

1) Display the URL they were looking for
2) Look up the URL they were looking for in a database or flat file and redirect them to a new URL if it is defined
3) Use the URL they were looking for in an internal search engine and suggest alternate pages.

Any suggestions based on experience would be appreciated