[Plugin: Redirection] Issues with mass URL upload

I’m in the middle of a site migration from .net to WP which has left me with over 5000 redundant URLs to redirect according to Webmaster Tools.

After using Redirection with its bulk upload feature to upload a .csv with all of these carefully constructed redirects it seems like a number of them don’t work and the old URL throws up a 403 as a result.

We deduced that the Redirection plugin only works on URL’s that don’t contain a query string.

Also, as the old URL structure doesn’t follow a distinct pattern we can’t create simple rewrite rules and put them on .htaccess as this would take forever.

If you could please offer up some advice or recommend a plugin that might help I’d really appreciate it.

Ed