Hi Everett,
Thanks for your response. This situation has continued to develop since I posted my question.
Our positions for critical keywords has continued to improve dramatically with yet more improved rankings reported early this week and again yesterday. We're now #1 for 3 keywords, 2 for a couple and 4 for a few more. Increases for additional keywords also.
Positions in Bing and Yahoo have gone up and down by relatively small amounts, mostly down this week but still holding on page 1 for those I care about other than "Gina Fiedel" which dropped 5 for Bing and Yahoo this week down to #14 and up to #6 on Google.
Immediately after I first posted this question, we did change one of the more worrisome site-wide citation links to the name of our company only (removing the keywords from anchor text), but left it in the footer for the time being. -we didn't do more due to internal issues that aren't worth mentioning here or I'll start venting- although, as time has gone by and we're doing so well, I'm afraid to rock the boat even though I know the advice from Russ and Mash was otherwise and I'm kinda embarrassed we haven't gone after it thoroughly yet. I guess I also felt that spacing the removals might make sense. The positions did drop a tiny bit when we did that but bounced back and as I mentioned, are continuing to improve.
Now to answer your question directly, Everett: We never received any messages in GWT and had no proof of penalty-manual or otherwise, so we did not file a reinclusion request. Our company name continued to rank #1 throughout the whole thing. It was only a couple of keywords that were effected. I now feel it may have been a manual penalty for those keywords (see below).
More info:
Just prior to the bounce back I found and got removed some inbound links that were really spammy with duplicated content in an article supposedly authored by an employee that never existed, a completely fictitiously named and imaginary person. (thank you http://www.linkdetox.com).
I also believe I overused those keywords on our Home page and had obviously re-wrote that right away but further tweaked it just prior to the bounce back.
Probably most importantly is that I started a blog and have been adding thoughtful, quality content and engaging much more on social sites and promoting the blog posts on social sites.
I am happy you chose to respond to my question at this belated time because it's a whopping good reminder of Russ and Mash's (and now yours as well) advice......
Oh! And one more thing! We will not continue putting site-wide footer links on client sites when we launch them. We will NOT be perpetuating that mistake.
Thanks!