MarketPress help needed

Hi guys,

I recently updated my client's site to the latest version of MarketPress and a bunch of stuff got messed up. The old version was from when MarketPress was $19/month instead of being included with the WPMU subscription. So it went back a ways.

Once I updated none of our 122 products were showing.
It prompted me to update the database which I did and the products appeared to come back.

It also prompted me to either use the setup wizard or go through the steps manually. I opted to go through manually and ended up just using the defaults which looked like they might be what we had originally because it showed a specific tax rate. Once completed I checked the site and noticed the following right away.
If you go to Shop in the navigation bar then click on either Dermalogica or Clear Start, then click the Shop Now button, it shows Page Not Found.
If you go to the Product Index page under Shop, it has multiple links. The first three do not work. The other direct links to products do work, but the product information itself is missing images.
Can you walk me through what I need to do to get all those things working again so I don't mess anything up and do it correctly? I can give you access to the admin dashboard if needed and my phone number if it would be easiest to go through this over the phone.

Thanks, James