Hello cdesnoyer,
I would advise you to leave the old version in place until you are sure that you are not going to need it.

Ledger 90 allows you to retrieve information from your prior year backups BUT you may need to post Year end adjustments in the prior year data so that the ending balances for a year will match up to the opening balances for the next year. Ledger 90A will not retrieve from data that has been converted to the 90A format.

You will not have problems with your other modules. Ledger 90 is capable of recognizing and retrieving the subledger batch files created for earlier versions of Ledger.