I am trying to use Google CSE for my website however without any success as it is not able to find half of the pages?
what could be wrong?
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Have you set yourself up in Webmaster Tools, and ideally submitted a sitemap also? Within the tools admin, you'll be able to see a lot of information about how and how much your site is generally indexed as well as things like crawl errors that will start giving you some idea why things might be missing.
Also, have you tried triggering an on-demand index?
Make sure every page is accessible through static links (
<a href='...'>) from the homepage directly or indirectly (i.e. homepage to page A and from page A to page B...). You can also (but not instead of) submit a sitemap to the webmaster tools.
Also, give it some time, Google doesn't crawl all at once. It "assigns" some time and bandwidth to each site, so it may crawl a big site in a period of weeks.