@syd
Welocme to bikers world. As some members mentioned above One of the reason of discomfort is just bcoz u r not used to riding bikes & with passage of time u will adjust to it.
BTW in reality CG 125 is one of the most uncomfortable bikes available here in Pakistan even CD 70 is far comfortable than CG 125 & beleive me that use of soft suspension & seat will not increase comfort level but even decrease it. However as ur bike is 2nd hand & equiped with brand new seat so its quite possible that seat used is of poor quality or suspension of ur bike might be the ruined/repaired one so get these both things checked by mechanic & got them replaced or repaired if these r not of appropriate grade.