Hello Rahul,
I suggest you to go for confirmation along with auto GR, backflush together. Also let the activities be posted along with confirmation. This is the best possible way out for this.
May I know why do you post activities with confirmation at the month end?
If you still want to post activities separately at the month end then I suggest not to post any activity at the time of confirmation with auto GR & backflush & to post one more confirmation with yield as zero for posting of activities at the month end. In this case system won't help for calculating activities as yield is zero. You will have to enter the values for activities manually.
Hope this helps.
Mangesh S