I have no idea what your talking about and I get the feeling that you don't either. Google custom search allows you to have a google search bar on your site while allowing you to make money from those search pages. While googles custom search algorithms changes SERP's based on individual users preference. In either case I have made more money from both of these features and havn't seen any negative effects thus far. I don't think resubmitting will solve any indexing problems and I believe your SERP problems can be attributed to the processing of the new PR display and normal movement with rankings.
Did the "built in" search engine that you replaced with a Google CSE, dynamically create and add pages to your sites index? If so, what happened to all the pages when you removed that search engine? Cheers James
Well I didn't deleted the built-in search engine, I just left it on top of my page. I placed the Google CSE on my sidebar like a widget just to test it out. So it's like people could choose if they want to use the Wordpress search (With Search-Unleashed plugin) or the Google CSE. I didn't edit or remove anything on the built-in and everything is intact on the database. Could this be a meta problem? Should I edit my meta tags or something? Thanks
Google CSE helps your website to get more traffic, it makes your website a lot easier for the googlebot to access. I don't understand how it could of had a bad effect on your traffic, Maybe it was a typical SERP fluctuation.
Edit your meta tags to what exactly? Why do you think there is a problem with your meta tags? have you recently changed them? Have you tried asking at any of the Google groups? You could try the webmasters help group, or the custom search help group, but you will most likely need to post your URL. Cheers James
Have you checked your backlinks? It's highly unlikely that your traffic was adversely affected by google custom search.