Hi Ash,
Take a deep breath
You have a couple of things going on including the change in site structure as well as moz and GWT data telling you various things. so the first thing to do is figure out what exactly each tool is telling you and why. Then you know what you need to fix.
For the moz report, you should check out where the 404s are coming from by downloading the report as csv and opening in excel. Filter by 404 errors and on the left column you have the error page and the far right column the page that linked to it. It is likely you have links to old pages on a page (or pages) of your new site in which case you should adjust these links to reflect the new architecture. That should take care of most of the 404's but of course you need to see the exact pages in the report to know for sure where and why the errors are happening.
For GWT I would think that maybe your old site had a sitemap and the new one does not? I do not see a sitemap at /sitemp.xml. This would potentially account for the 163 submitted but only 2 indexed. Google does not easily forget old submitted sitemaps so if it still has the old sitemap in its 'memory' and the new site only has 2 of the same urls, you would get some numbers like what you see. I would create and submit a new sitemap reflecting the new architecture and see what that does for the numbers. Be patient, it can take a few days or even a week or two for google to completely spider the new architecture. Of course you should also 301 redirect all the old page urls to their relevant new pages if you have not done so already.
Hope that helps! Main thing is to cut the data into more understandable chunks so you can get a better handle on what is going on.