Just Joined

Hey Guys,
I am new here and of course, I joined because I have a problem. First, let me tell you a little about myself and then my atv. I am an auto mechanic by trade and have been for about twenty-seven years. I know some about atvs and understand there terminology very well but I'm not technically trained or know them in detail. That is why I am here. I hope to be able give advice as well as receive from this sight. I have a '07 Honda Rincon camo, bought it new in '06 and except for 27" tires it is still all stock. I believe that I have about 150 hrs on it now but the meter is off. I had to replace the instrument head, only because someone’s face went into it. I never had any problems, until now. I have changed all the fluids more than necessary, only because I can, being a auto mech I get fluids very cheep and do all the work myself. I use 10w40 non syn non energy conserving oil and premium limited slip 75w90 in the diffs. This is what my dealer said to use so I stuck with it.
Now with the problems that I have. The three most important are, first I have a loud grinding noise in the engine/trans, only when applying the rear brakes, hand or foot, in 4x4 or not, and this does not happen when applying the front. However, it is definitely not in the brakes. I have taken them completely apart cleaned and lubed the slides and still have about 90% pad life left. I have read that the rear rotor comes apart at the rivets so I welded the rivets, inner hub, and rotor together so that they do not move independently. Noise still there. Second, another noise is on the left side of eng/trans sounds like metallic rattle or med. pitch whine. It goes away when I shift into gear but will reappear with light throttle when cruising at any speed, not accelerating and not decelerating. Third, I believe that the cam chain is loose. I also have alot of tapping noises. Valves have been adjusted properly. I am pretty sure I'm going to have to tear this thing apart, not a problem, but I'm not sure what to look for when I get it apart. Can anyone give some advice on what could cause these noises? And if they can be fixed without pulling the eng. I called the dealer and he said the rincon have a lot of noises. I am sure these are not normal.
Sorry for the long post I will try to be shorter in the future. Thanks