Need help with friends bike making terrible racket

Hi all, I need some advice. I'm trying to help out a friend who's bike suddenly started making a terrible noise while in my possesion. It is a 1997 XR650L. We were driving along a dirt road fairly slowly and came to a stop, the bike died at idle which is very unusual for this bike. Started it back up and went a little further then it died again. This time when it started back up it was making a loud knocking noise, it is there at idle and when you pick up the revs, seems to be louder on the right side. We shut it down immediatly but I don't know what is wrong. It is blowing a small amount of smoke when cold. I took off the valve covers and checked the clearance, it seemed to be ok *see below for my question on that. I was curious if oil was getting up there so I turned over the engine while taking each of the covers off one at a time. The two on the left sprayed all over and made a terrible mess, the two on the right I couldn't really see if any oil was there at all. Is this normal or should all 4 make a big mess? Anyone have any ideas what is wrong and what I should look for first if I start to take it apart?

*about the clearance. On my bike I have always kept sticking feelers in until one didn't fit and the one below that I declared was the clearance. The manual for the XR says to use the one that drags a little. That seems so ambiguous, there are about 4 different feelers I could say that about. How do you all go about checking the clearance?

Thanks guys!

I hate to ask this question, but you didnt mention it. Did the bike have enough oil in it when you were riding?

Oh yes sorry good point! Of course the first thing I did after hearing the noise was to check the oil. It was splattered all the way up the dipstick so I figured it couldnt be too low. I checked it again after getting her back home and it was down about a half to 3/4 of a quart

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