Azure web app file permissions

Azure Public IP's are IaaS objects. The association is from NIC to Public IP not the other way around. That's why you can't see a way to associate an IP with anything.

My guess is that you're trying to associate an IP address so that you can have a custom domain associated. Instructions for that are here: https://azure.microsoft.com/en-us/documentation/articles/web-sites-custom-domain-name/

If you did not that already, try to place your DB and WebSite in the same region. AlwaysOn is the good way to do, but it looks like the problem is more sophisticated and there should be a more troubleshooting. As Sam suggested, the mode is important as well because of various limits and throttling, but if you say that the load is low, it should not be the issue.

I would propose you to go and fire some SQL troubleshooting, for example, that (thanks to Liam Cavanagh) query will show some top queries that take a longest elapsed time.

Did you try a local database or a database in the VM, by the way?

SELECT TOP 10
qs.total_elapsed_time / qs.execution_count / 1000000.0 AS average_seconds,
qs.total_elapsed_time / 1000000.0 AS total_seconds,
qs.execution_count,
SUBSTRING (qt.text,qs.statement_start_offset/2,
(CASE WHEN qs.statement_end_offset = -1
THEN LEN(CONVERT(NVARCHAR(MAX), qt.text)) * 2
ELSE
qs.statement_end_offset
END
- qs.statement_start_offset)/2) AS individual_query,
o.name AS object_name,
DB_NAME(qt.dbid) AS database_name
FROM sys.dm_exec_query_stats qs
CROSS APPLY sys.dm_exec_sql_text(qs.sql_handle) as qt
LEFT OUTER JOIN sys.objects o ON qt.objectid = o.object_id
where qt.dbid = DB_ID()
ORDER BY average_seconds DESC;