I just got back from an unexpected trip and so am catching up.
First a few notes.
The upgrade works more or less as follows. Understanding this process is the key to understanding when/where restoring from backup is helpful vs rolling back the upgrade (which is generally preferable in a case like this):
1. We run some tests on the data. Where there are problems we try to give the opportunity to fix them.
2. We move the data to the side (from the public schema to schema lsmb12) and create a new database schema for LedgerSMB 1.3
3. We populate that new schema with data from the 1.2 instance.
If you run the sql/upgrade/1.3-1.2.sql it will drop your 1.3 data and move your 1.2 data back to where it can be seen. This restores you to the point just before step 2 and the db will continue to work with 1.2.
Reading the problem this does not look like an extension problem. In general we don't have an easy way to handle pre-9.1 contrib modules and post-9.1 extensions without throwing errors on both sides, so the errors look normal to me. The error seems to come from the lack of a customer_id field where one is expected.
In the upgrade script the first mention I have of customer_id is with the import of ar records. ar.customer_id is a very important column, but it doesn't seem to match what you are trying to do.