Don't know if you've already tried this, but my favourite way to clear things like this is a 'receipt' acknowledging 'payment' of the various items that add up to zero.

Always start with making a full backup and storing it safely away from your computer. The way to clear some of these customers would be to remove transactions up to a set date if fully paid. When there are no transactions for the customer then it can be deleted. Same holds for vendors. Remember that financial records must be retained for six years plus current for CRA audit purposes so I would not delete any data unless it is more than six or seven years old. 

this is what i tried to do, the error listed above is what it gives me 

transactions cannot be deleted, data not found of some type of error like that. There are literally hundreds of 'stuck' transactions

Did you go to Maintenance > Clear Data and then from the drop down list chose the one you want. You possibly want the second one in the list which will then give you a further choice. You can set the clients' data to be deleted, one by one or all. 

There are controls, but again I caution to make a backup before trying anything and then test your results.

I have weekly backups so im not concerned about data loss. I will try that, I really want to get these transactions cleared it is such a nightmare!