Hi Trambak.
You're really entering the fuzzy world of performance tuning here.
You need to identify a period of low activity, when you're not loading data. It sounds like you're already creating one with a nightly 'maintenance window'. If you have two conflicting requirements -- do all maintenance inside the maintenance window, and that window of time is too short to complete all the assigned maintenance work, you need to start looking at a hardware upgrade of some sort.
Now, a thing about runstats and CMOD... Since CMOD is an archive, tables rarely (if ever) change, except for the addition of new data. Because of this, access methods are generally the same -- find the table containing the relevant dates, use an index to eliminate the majority of the table, and search for your results inside that set. In this scenario, runstats doesn't really help that much.
The ultimate solution for you might be to simply run 'runstats' less frequently -- perhaps on the weekend when usage is lower, or your maintenance window is longer.
Good luck!