Hi Anthony,
It sounds like your on the right path. Make sure the site has good, quality, optimized content. Analyze the link profile and deal with the issues you find. Create new quality content that is remarkable and get it in front of people via social networks, guest blogging, etc.
It's not a quick process, though. It sounds like the site you are working on was in pretty bad shape, dealing with both Panda and Penguin issues, including spammy links and over-optimized anchor text. It's a lot to fix and Google doesn't just bounce you right back to where you were. First, Google wants to see that you are really back on the straight and narrow and aren't going to try any more spammy stuff. Secondly, the rankings the site had before weren't legit. The site had them because of manipulative strategies which are no longer working. Think of it this way...
If I weighed 250 lbs and I wanted to lose weight. If, instead of working out and eating right, I decided to lose weight by adjusting the scale and I adjust it to the point where it says I weigh 200 lbs. The scale may indicate I'm losing weight, but I'm not. It's fake. If someone then comes in and fixes the scale so it can't be adjusted, I shouldn't expect that the scale would still say I'm 200 lbs because that wasn't real. It'll say I way 250 lbs (or may more). In a similar way, if you manipulate the search engines to give certain rankings instead of getting those rankings by creating great content and getting links naturally, then when the search engines change so you can't manipulate them anymore, you shouldn't expect to keep those fake rankings. You'll be back to where you were at the start, possibly worse off if you get penalized.
So, you are on the right path, but you (and your client) need to have the proper expectations. You may have more issues to deal with and you probably need to be creating new, remarkable content so people will share/like/link the content and build the site's authority up...the right way.
Kurt Steinbrueck
OurChurch.Com