I came to a company that already has a fully grown project... but coders that worked here before me didn\'t follow conventions and didn\'t use parametrized SQL queries... as
In order to really do this right you need to just divide up the application and go through it one module / page / class / whatever at a time.
This will allow you to not only fix the problem, but also to become much more familiar with the code base in general.
UPDATE
Based on the comment I wanted to add one more thing:
The only thing a tool can do is say look, here is some unsanitized inputs... Which, most likely, is going to be just about every query in your app. Which means you'll have a list of about 3000 or so files that need fixed.
At that point the only thing you can do is designate a day, like Friday, as Fix Sql Day. Divide up the work and then have everyone spend a day (or even just a couple hours) rewriting the queries on a few pages.
At some point you'll either finish or find enough other things wrong to determine if starting over is a good idea.