I'm not much further forward than yourself in upsizing a complex Access 2003 application to SQL Server 2005 and I also have a very large list of errors generated by the upsizing wizard, so I certainly can't claim to be an expert on the matter.
However, I am well aware that it can be quite a complicated process to make this transition successfully. The devil is in the detail and there is no way that the wizard is going to do all the work for you. For example, you may have quite a bit of DAO code to convert to ADO. You need some good reference books to help you make this journey.
I can recommend the Access 2002 Enterprise Developer's Handbook by Paul Litwin, et al. I think it is now out of print but you can get a used copy very cheaply on Amazon. No doubt there are plenty of other good books out there that are a little more up to date - though the principal differences between Access and SQL Server have probably not changed all that much with SQL Server 2005 vs SQL Server 2000.
You may also find it useful, as I have done, to start by using Microsoft SQL Server Migration Assistant for Access to do a test upsizing of just your BE database. There are far fewer errors when there are no forms, reports and queries to upsize! Getting the basic table structure fit for SQL Server might help to reduce the error count when you run the wizard again. Another useful thing is to eliminate all unnecessary items from your FE and BE, i.e. get rid of any out of date tables, queries, reports and forms.
David
