Google is not liking the fact that I have numerous synonym pages, where the only difference is Title and Meta variantions, along with a chunk of content in a layer not visible on page load to the user.
I would highlight this issue as a major concern. We know for sure Google does not like duplicate pages, nor hidden content so these are going to be your issues.
What Google wants to see is each page offers unique content, and the content is prominently displayed to users up front. Burying the unique content in the footer, hiding it with java script and any other form of shell game will leave you quite unhappy because sooner or later you will wind up on this Q&A asking what happened to your rankings.
As for the rest, try to keep your linking natural and don't force it.
As you mentioned, it takes time to see any adjustments truly settle into the rankings. Some differences might be obvious the next day. Others may take weeks to appear. Google samples your site, and the web, in pieces. Site owners often make improvements to their site, see something they don't like in SERPs, panic, then make other changes as a result.. Don't panic.
You need the ability to understand SEO at a level where you have confidence in the changes you are making. Make the proper adjustments then just watch. Don't touch your site for 30 days and then check the results. If they are not to your liking, look for other adjustments. The other alternative is to hire a SEO who can do the work for you. If you do hire a SEO, understand we don't have magic wands or buddies at Google. The same rules apply to us as well.
