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It looks like you're 301-redirecting you're root site to the "/index.php" version of the page. The problem is that you're linking to the root "/" in the navigation and most of your inbound links are probably to the root. So, you're sending a mixed message about which version is actually canonical. I would stick to the root, personally. The non-www vs. www issue is also in play, but I think it's a secondary problem.

I'd use Google Analytics or another analytics program and track your traffic. Traffic increases, you've made progress.

Often I see the clain that someone is ranking well with heaps of crap links, but usually among those crap links they have a few good ones that is giving tem the rank, but are hard to find among the crap

what type of writing worked better, highly technical or conversational what length of article worked better what keyword density worked better (don't concern yourself too much with this) Different niches will require different things. Once you've done enough to get a little search traffic, expand on the post that worked, write a similar post about a slightly different topic. Basically, throw some stuff at the wall and see what sticks.