1) the page extension between .php and html is not a variable that will impact your page rank. Either way, the pagerank will be the same regardless of the page extension
2) I'm not sure I understand. Are you using php includes to display the article? Either way, do a search in google for [site:
www.yourdomain.com] to view the pages google has listed. Then select the cache link in google's results for the url in question. That cache (view source if not sure) is what google has spider/included. The url will have pagerank, but an include php is considered as part of another url as the spider/visitor views it.
3) PageRank is a formula based on links. Yes, if you want the pagerank to be the same ... then the link structure should stay the same. One approach is ... if your home page has a lot of links going to it, and thus pagerank you can also get links to the archive page which you want to increase the popularity/pagerank.
My two cents, don't worry about pagerank too much and realize that the pagerank displayed within the toolbar is not very reliable and only one factor of many.