Would you try 4GB RAM tuning? By setting "/3GB" switch in boot.ini,
an application process can allocate more than 2GB memory.
Then, comment out "innodb_buffer_pool_awe_mem_mb" in my.ini,
and set "innodb_buffer_pool_size=2500MB", for example.
But my worry is that windows 2003 server standard edition officially
support /3GB switch only for Microsoft's tested applications,
like MS Exchange Server or MS SQL Server.
For details, see
http://support.microsoft.com/kb/291988/en-us.
So I think your ways are,
a) Test /3GB switch, and judge to use it or not.
b) Buy Windows OS which fully supports /3GB switch.
c) Buy EM64T H/W and Windows OS.
d) Buy Visual Studio, and recompile MySQL by yourself.
Ummm, it's really a difficult problem.