I've just upgraded from Marketpress 2.9 to 3 on my test site.
The first thing I've noticed is that the custom template files I created for v2.9 aren't being picked up in this version
(these are all in my theme's root)
The store looks to be using a simple page.php file for single product display.
Also a few other settings seem to have changed - do you have a guide for upgrading from 2.9 to 3.x ?