Grinding noise
 

I have an 2007 Yamaha big Bear 400 4x4. It makes a grinding noise that seems to be coming from the cylinder head. I took the timing cover off and idled it. the timing chain and sprocket operates fine without any play. so after that I took the camshaft and bearing off and they seem to be like new. No parts seem worn. Put it back together and stills made the same noise. I then pulled off head and cylinder and they are like new. The piston, rings and rod bearing are good to. Reassembled and still here the noise when it running. The noise is there when driving forward, backwards, or in neutral. What is the problem?

This is one of those "could be anything" questions, but did you check if the timing chain guides are worn, or the fixed one not properly seated. I managed to get the fixed one wrong on a Bruin and only found out during the next rebuild..

The chain guides weren't worn. Do u think the rocker arms and rocker shafts could be worn, or maybe the valves need adjustment? Other then that I think I've checked everything except the crackshft bearings.

Cam lobes, rockers etc, can wear, but I would have thought you would have noticed this when you had the cam out. If I remember correctly the bearings on the cam are ball races? These can make a lot of noise if a ball is chipped, without showing signs of play, however if you spin one by hand and get that noise, replace it.

Grinding noise
 

Last night I checked the valve clearance and they are within range. I then took out the spark plug to make it easier to turn by hand. It does not make the noise this way. However I do remember the front cam bearing have small, tiny scratches on it last week when I checked. Also, the cam lobes do not have and wear on them. How do I pull out the cam bearing that's way in the back without taking apart the whole thing?

Not sure how you get the back bearing out, probably internal expanding slide hammer. I would have thought you would still get the same noise from any cam problem, with the plug out though.

Grinding noise
 

What if I pack the bearing with grease and see if the noise goes away after start up?

Worth a try, probably wouldn't totally silence a chipped bearing, but may muffle it enough to be able to tell if that is your problem.