I have a lot of experience developing databases on SQL Server.
Also I was worked as DBA, so I could help you with your problem.
Actually there is no overhead from NT-auth, I think your problem persists in queries from Acces backend.
Probably there is full-table reading instead of filtering queries.
Also your backend may block tables with long-transactions.
I need estimate your queries on SQL Server to find issue.
After I will find issue I will propose you next steps and do some step for myself.
For example I can create missed indexes and rebuild some view/stored procedures if any.
Damn freelancer again broke milestones feature. So I will put it here:
1. Find issue. I will use SQL Profiler and internal monitoring features.
2. Write down issues with some steps to fix
3. (re)build missing indexes and rebuild view/stored procudres