Recovering WP site from malware infection

Closed - This job posting has been filled and work has been completed.
Fixed Price
Deliver by - November 22, 2012
30
Budget

Details

One of my site was infected with a redirect malware.

While i was able to remove the affected files (htaccess etc), I might have created other problems. While the main site loads correctly now
http://shopthevalley.ca
all other pages show a 404 code despite being there in the dasboard.
also while all my plugins are still on the server in the directory they also have all disappeared from the dashboard.

Strong WP/server/database skills a must

I need these issues resolved ASAP

Please state your diagnosis