The engine oil system is pretty simple and not easily broken or clogged.  About the only thing that can go wrong with it is if you took the clutch basket off and didn't get the drive gear or pin back together properly....the pin can fall out easily.  Generally the piston/cylinder is the first thing to go when the oil pump isn't working.

The most likely scenario is the cam/rockers have been damaged from using oil without sufficient levels of ZDDP and the exhaust rocker and cam lobe have been damaged......or your idle speed has been set too low and adequate oil flow has not been maintained.  Check your valve clearance and see if you can get a peek inside to see what the cam looks like.  If your clearance has gotten significantly over 0.004-0.005 it is an indication there is excessive wear.

One other possibility is a loose flywheel nut.  This happened to my bike when I first got it.  The ticking started when the bike only had 400 miles on it and was a horrible knock by the time it had 1,100 miles on it.  The noise was worse at idle and smoothed out at speed.  One member recently went through this issue.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1739410713