Make sure you have some good analytics software installed on your website. You will want to know where your traffic is coming from. Is it coming from social media, referrals, search engine queries, or is it direct traffic? It will also help you determine where people are getting lost, or dropping out of the funnel. It can also help you determine what approaches, content, and CTAs are the most effective.
At the end of the day, webmasters just need to know their sites: chances are your analytics tool is more like a person than a software package, and will classify traffic in irrational ways. I’ve stumbled across website traffic originating from diverse and confusing sources being classed as direct — often requiring a considerable amount of thought and exploration to work out what is happening.
Another tip you can use is just reach out to the prior agency and say something like the following: “We realise you were using link networks for our website which has resulted in a Google penalty and loss in business. Can you please remove my website from any link network you have built?”. If the prior agency is decent, they will remove the links from the network.
Unless you have an invite, you can’t comment or submit a new product to PH. Even then, if you were to submit yourself, the likelihood is that you’d miss out on a lot of traction compared to someone influential on PH submitting. You only get one chance to submit to Product Hunt so you’ll need to identify someone who would be interested in your startup that also has influence within the PH community. To do this, go to Twitter and search the following query in the search bar:

I'm thinking about "less to do" (linking-social media) sites with physical products … Amazon and other merchants. And adding a PPC campaign instead of using social media and constantly toiling away building links and writing articles. Is there an easy way to get sites like this to rank while profiting with some paid traffic? Your opinion on this dilemma .. SEO vs PAID traffic or both would be much appreciated.
I would also advise to continue doing what works. If something you have rolled out generates great traffic and links bring out a new version of the content, for example the 2012 version worked effectively bring out the 2013 version of the content. Another effective strategy is to make the piece of content into an evergreen article which you add to over time so it is always up to date.
Organic is different. Matching keywords to user intent means you may be present in many searches. The user may find you consistently, and once they get to your site, they are more likely to stay. Organic users are still your best long-term customers. In my experience, they have lower bounce rates and more pages visited, and they are more likely to return.