@SarahFlo
I would ignore any posts from QB employees on this. As you can tell by @Jelayca V 's response, they do not have the experience to fix this. They just post canned responses.
Just to clarify, it isn't that you used Undeposited Funds, it's that you didn't use Receive Payments, correct? If you had used Receive Payments, at least you would know who paid what and it would just take a little extra work reconciling the bank statement to group the deposits. I just want to confirm that I'm understanding that correctly.
At this point, you don't have a lot of options. For cash payments, if you didn't use Receive Payments, there's no way to determine where the cash came from short of contacting customers. If they were checks, I think your only option is to look at images of the cleared checks online and match the names on the checks to your customers.
To clear A/R balances, you need to assign an A/R credit to each customer. That happens automatically when you use Receive Payment. Or, you can assign A/R to the deposits you recorded. Each customer needs their own A/R credit line on a journal entry or deposit. There's no way to clear A/R balances other than by doing it by individual customer.