Hi Samid
1. On your ECC system when system performance getting slow or degraded, check the following transaction codes to know the system status
SM66 – To check over all global workprocess status, any table keeps on reading or getting struck?
SM21 – Check the any error log
ST02 – Memory / Buffer usage?
ST22 - Any time out or DBIF ... Dumps?
2. Most of the time Z-reports are running long time. Due to this normal transaction users are getting affected. For this you can enable the transaction code ST12 trace check the overall DB & ABAP program usage.
3. On your Cluster environment one node can have DB & Application instance and another node can handle the end user transactions. Since the windows 2003 server end of support on this year try to upgrade the existing system to either windows 2008 or 2012 with Failover cluster.
4. On your MS SQL DB have you define the 30% of memory for DB? And also you can refer the SCN link how to tune the MS SQL DB
Tune your SQL Server SAP Database
BR
SS