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I see suplpemental results in Google that were last crawled in February 2004 - it's no wonder they have such a big index.
Another option would be to use 301 status HTTP redirects - but Google sometimes does strange things with redirects so I would probably avoid that if I could.
So you want Google to drop the old URLs, and crawl the new URLs.
One common problem is that if you remove all the old URLs at once, some of them are no longer linked to. This can cause Google to keep them for a long time as supplemental results.
> 2) What type of redirects should I use within the php files (headers, meta, or javascript)?
If you were going to use redirects, 301 status HTTP redirects would be best. If your PHP is on Apache then you'd probably find mod_rewrite easiest, otherwise you would be looking for the relevant PHP [webmasterworld.com] code to set the HTTP headers.
Personally, I would just upload replacement PHP files with links to the new URLs.
> Also, if I was to use duplicate phps as just pointers to the new htms, should I then keep these php pointers indefinately?
I would expect that you would only need to keep them until Google has removed the duplicate content. Of course you might also want to think about links from other sites - and bookmarks.