Too many files in folder is not related to MonoX but to NTFS, so do you have a large amount of files in the Log folder ?
The following error seems to happen to often:
2016-05-07 18:53:24,920 [37] ERROR MonoX [BaseHttpApplication] - Application Error
System.Web.HttpException (0x80004005): This
is
an invalid script resource request.
at System.Web.Handlers.ScriptResourceHandler.Throw404()
at System.Web.Handlers.ScriptResourceHandler.ProcessRequest(HttpContextBase context, VirtualFileReader fileReader, Action`2 logAction, Boolean validatePath)
at System.Web.HttpApplication.CallHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute()
at System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously)
It happens every 100-400ms and this could potentially flood your log files and Log folder causing the NTFS to be slow while accessing the folder, can you please check ?
Also do you have SQL server running on the same machine as Web ?
Regards