Okay we could nail down the issue, it was the intake valves clearance being nil which checked, this caused the bike to run rich and rough at lower rpm.
as per the manual valves needs to be done at 18K miles and my bike is 28K kms run as of now. its at the mechanic now and should get it back in couple of days.
the first cylinder was blowing air out at idle instead of sucking, above 2.5K rpm it sucked in like all other cylinders.
Hopefully i would be able to rectify this issue soon and this thread will help other members facing the same issue.

on the other hand was replacing my old chain sprocket kit, and noticed that the prev setup was 16-42 instead of 16-43. Put the new set with correct gearing, hope fully this will help too a bit