timing marks wrong?

hey guys
i have an interesting question.I have a 2002 660 grizzly.the timing marks for some reason are incorrect.A friend of mine a very experienced diesel mechanic was giving a hand setting my valves.According to the manual we were following we found the marks was wrong.So we pulled the plug used a rod to find tdc.set the valves to the gap according to the manual.I can only assume because i bought the bike used with no knowledge of its history.My guess would be the timing gears are not in time ,there for the timing marks is off. which brings me to this question,can i accurately set the valves?and would this be the reason the bike is so cold blooded on start up?