Are you using 1.x? or 0.7.x? 1.x is not ready for primetime use
judging by your PM link to your site, it appears to be 0.7.x.
It is connecting to the database fine and showing products fine, but when you click on them it gets page not found.
You mentioned that you disabled url alias, but I see it is still enabled so it looks like you are using 0.7.8 with the url alias bug. Any chance you can upgrade to
0.7.9 ?