hi,
only some suggestions.
Calling NAV Webservices a lot of response time is spend by authentication; try to authenticate using NTLM instead of Kerberos and force TCP protocol.
if you are using Kerberos with Kerberos tickets, check trusted delegation &SPN (duplicated, lost etc.); try to reset kerberos tickets (with purge)
NAV WS Standard Trace
You can try to activate diagnostic tracing for Web Services to identify bottlenecks
blogs.msdn.com/.../enabling-diagnostic-tracing-for-dynamics-nav-web-services.aspx
Try to install last NAV 2009R2 builds, some bugs have been resolved about WS Authentication
blogs.technet.com/.../microsoft-dynamics-nav-2009-r2-fixes.aspx