Ajax Angular JS SEO architecture consulting

We have a website that is using a customized joomla component as the base framework for the ajax pages. The data is linked from the json file to angular js. The javascript interaction is a combination of angular and jquery. The url structure is mapped via .htaccess to the regular joomla url. Our problem is Google is not indexing certain pages, basically any page linked from the ajax page. I need someone with awesome experience in the above platforms to consult on our one problem. If this is you, this will be the easiest money you'll ever make. I don't need you to do any programming, or to write code, just need you to tell me where we are going wrong. We have checked all the usual suspects - robots, blocking javascript etc. Google Bot renders the page ok. Says there is no issue with the page. It has even indexed the first ajax page but it will not index 2 links deep (basically any link from an ajax page will not be indexed). We have 2000 pages in our sitemap, Google will index only 100. We have plenty of crawl juice - google crawls about 3500 pages a day (my old website was 40,000 pages). homepage - crawled and indexed (standard php html page) first link deep - crawled and indexed (ajax page) second link deep - no indexed (all linked from an ajax page) I believe there is something about the links from our ajax page that is a problem. Can you quote with why you are a legend in this field of coding and what you need from us to diagnose the problem.