WOW! Scott, this is interesting! And here is my take on it!
I am taking some lines from your description! That says,
‘and they reported back that a server that had 20links pointing back to our server had crashed on Christmas Day and the links had been de-indexed from Google, they said give it 2 - 3 weeks and the links will be re-indexed and we should pop back up on google.’
I will question that.. if it is exactly what they said then in my opinion they were putting the link on the website that they can control and this can be a site of their network! If lot of links are actually coming from the network sites then I must say that Google was nice to you!
Changing the content improves your long tail but your main keyword dropped even more! In my opinion here is what you should be doing!
Remove as many low quality links as possible!
Get in to your link profile, get your hands dirty and remove it… you don’t have a choice or else the slap can be even harder!
Get more social
Google take social as a way to find the website’s credibility, get yourself active on social media accounts like twitter, facebook and G+
Create Link Baiting Campaigns:
Start the brainstorming process, sit with your marketing team and come up with any idea that is link worthy! Start a Quiz, Contest, Award or Badge! Something that allow your industry bloggers to talk about you and link to you!
Get Press Links!
You can even connect link baiting and press links if you are creative enough! Do something that becomes a story. Journalist likes stories, approach them and get a link from PR and news websites!
Start a Blog!
Share your expertise and start a company blog, it will give you a hard time but you will be able to get some great links, content that will eventually get you SERP benefits!