Wow, this is a very broad question and a bit difficult to think of how to give the most helpful/responsible answer.
+1 to UG's suggestion.
Also, it might be a good idea to confirm that you have already documented all of the business and process rules before removing those queries.
Even though this shouldn't be, it is all too common for the only place the business rule is documented is by looking at the design/SQL of a query!
Thus, don't remove your queries unless you've documented the process/rules/requirements somewhere, as you won't have a query to look at and remember - "Oh yes - in this case I want to return Nulls because the Accounting department wishes to know if there is an invoice without a payment", etc. etc.
Don't burn down the house unless you saved the blueprints, as problematic as those blueprints might be.
Even with backups, it's a good chance to create logical documentation to support starting from scratch again.
I commend you for recognizing the value of getting the foundation right. Painful but necessary