Update... I found a very good priced 250 top end from another inmate (thanks Rick !) so I figured I could accomplish a few things with it:
1- try a 250 for a while
2- have a spare in case I ever did pooch a cylinder/piston
3- see if the powervalve is the issue.
Well I mounted up the 250 top end in late fall and although it fired right up, and the same rattle was still there. So the loose pv in the 300 cylinder is still a mystery, and the bike has been in hiding since I had a foot operation shortly after that, then the cold fall was excellent for trials riding and recouperating the foot well into Nov. Winter then kicked in and I've only just got back to working on it. I've stripped the cases to find that Widebear was right.... the right side crank (ball) bearing is in real bad shape, very rough and a bit pitted. The left side roller seems better, but its seal had some gook in it that appeared to be silt/mud from the water. I think the oil passage to the bearing must have been plugged with the crap causing the bearing to get oil starved and destroy itself. New crank bearings are ordered and also the bearing behind the clutch (a 6205 bearing) which is obviously unrelated but it also is on the rough side. I happened to have another new quality NTN 6205 bearing kicking around that I had for either a wheel bearing or an idler wheel for a snowmobile, and it doesn't seem much smoother. I cleaned them both out and blew out with compressed air but it just doesn't seem to be a very smooth running bearing. The new one is slightly better but are they supposed to be that loose rolling and rattley? The other bearing on that side is a similar sized 6203 and it plus all the other little bearings in the case seem much smoother, so I'm looking for an alternative.
3 lessons learned ...
- will now take a different route no matter what to avoid waist deep water
- don't shut off the motor to walk the bike during a deep water crossing
- once spooge starts coming out of the header/cylinder junction get new O rings (probably where the water got in)
Will report again once its all freshened up.
edit: GMP - the linkage and actuator are all fine. The problem is that I can hold the flapper steady and still be able to move lever arm several degrees. The 250 pv is rock solid with no movement. I'll get that 300 pv out some day to find its problem.
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