You need to identify how many Accounts, and Contacts have already been created via Lead Convert. And then "somehow" identify which Opportunity records need to be attributed back to those Converted Leads.
You also you need to start having your users create Opportunities via the standard Lead Conversion Process, to prevent this from getting any worse than it already is (which is probably pretty bad) .
By not creating Opportunities via Lead Convert, you've created a MASSIVE data/information/knowledge void, one that is going to take a LOT of effort to fill in, like a pothole that's been ignored and only gotten increasingly worse over time. Until finally one day the townsfolk are staring at this massive canyon in the middle of Main Street, and one of them says "I'd like to drive to the Donut Shop on the other side of town, how do I get there?"
