I agree, 2% of the links is too small of a number to worry about. no real help either way. And yes, that 950 strike is a big one.
I disagree about 3-6 months though. Perhaps I misunderstood but I though there were <100 pages in the "home" section and that's what we are talking about. That should be easily devoured and be updated in the index in just a few weeks since you have a decent number of links. Sandboxes won't apply to this since your site already has decent authority.
If the pages aren't indexed work on a sitemap of them (either rolling on the homepage or static as a link). If they are, try and build a few quick and fresh links to them ... ranking in no time.
For FHSD$$$ ... what I suggested is a light weight version of
this. I know you are not talking about his extent of automation but I feel what Eli says about cleaning up the links makes total sense. You are basically distancing your self 1 step further away from a "bad neighborhood" if that's what you guys consider link trading to be.
For both of you guys, How's working together on this going? How many hours do you work together on this daily? My wife has plans to come home shortly to help out with my stuff, she brings nothing technical to the table but is insanely organized and well educated in customer shit that I just don't care that much about. She's going to bring a different element to my work all together.
I'm personally worried about her hurting my creativity & productivity. I hate to say it but she might be too high maintenance (:]) for me to get anything done. For the hubby, PM me if your answer isn't suitable for public viewing.