This thread is getting a bit long and I dont see all the relavant information needed to properly troubleshoot the issue so let me try summarize the sequence of steps your portal/cart has been thru and please fill in the blanks where requested below
1. Originally your portal was running DNN 5 and SmithCart 3.? (please fill in the version of the cart you upgraded from I dont see it mentioned in the thread)
2. You upgraded your DNN Portal from DNN 5 to DNN 6. As we all know upgrading major versiosn of dnn is not a perfect process and can create errors in your dnn portal which might only be manifested in the cart since the cart is such a big module tapping a large portion of the dnn api. So it is a possibility that the cause of the cart error you reported could be related you a bad dnn upgrade. Keep in mind I am not saying this is the cause I am saying its a possibility.
3. You backed up all the data in your smithcart tables; products, categories, orders, etc to a backup database. Did you use the SSMS export option to backup your cart data or did you use another tool?
4. You deleted all the smithcart modules from the dnn host - module def screen
5. You confirmed that all the tables and sprocs with the prefix of "smith" were completly removed.
6. You installed the smithcart v4.58 and added the buynow module to your store page and configured the buynow settings
7. You imported the cart data you backed up in step 3 above (please confirm what tool and procedure you used to import your cart data)
8. You ran update statements on the cart tables to update the tabmoduleid with your new tabmoduleid
Please confirm.