Wow

pull it all apart with that.

cliff

 I cannot tell what is going wrong other than it does not look right.  Right hand side looks like it turned inside out, unless it is really odd looking seal.  Looks to be a gap between the lip and the crank. Never saw anything quite like it.  Is it in right way around?  Does it look all bent up like in the pic in real life? It does not look to be square in the bore either.

Edit. Disregard my uninformed gibbering.  Curiosity made me go find a parts book.  I see the seal actually runs on the gear.

As for the rotor and crank taper.  It would behove you to remove the key.  Put some fine grinding paste on the taper and lap in your rotor to the taper for a minute or too.  You will then be able to check the fit twixt the two parts.

Two bad things happening simultaneously



asco

In my opinion--seals aren't the cause of your problem.
looks like the mag side might have the outer spring broken so hook it off. The outer one isn't much more than a dust seal compared to the inside spring.
Right side looks ok & no leaks.
Saying that because were looking for a serious cause of your backfire or explosion.
Always good to do seals--but!!.
Also regarding the mag key--you don't know how lucky you are. Better go buy a lottery ticket, you'd be a winner. Loose flywheels never turn out good.

.

So, I got the damaged piston and rings today, and cleaned up the area of damage so as to get a better look.
Behold . . . . . The ring locating pin was still in place as I'd suspected

After looking over the damage under 20x magnification, I will now share my theory as promised in my last post.
Going back to the Previous Owner, this is what I believe happened

For whatever reason, this standard size cylinder had been removed ... and then reinstalled, but with great difficulty

It appears that the lower ring snagged on the top of the intake port as the cylinder was lowered over the piston.
P.O. proceeded to try and "violently" force  the issue, not realizing that the ring was sticking out into the port hole.
I say violently, because it had to be a lot of force (dropping or banging ??) to break a small chunk of aluminum out of the bottom ring land.

I theorize that the ring got bent (not broken) at this point and the frustrated installer looked inside the intake port and discovered what was going on.

Then taking, what I believe was a flat blade screwdriver ...
he started trying to knock and push the bent ring back up into it's groove.

There are obvious scrape marks on the piston, as well as blunt force indentations, from the screwdriver blade.
There's even a screwdriver indentation in the back wall of the ring land, where it obviously slipped off and past the ring.

At some point, he realized he needed another ring . . . to start over again.
Piston appears to have been touched up with a power rotary tool, file, and/or sandpaper .... to knock down the high spots.

Second time was a charm . . . well, maybe not  
.... ring did not move freely in the damaged area and was pushed into place ... firmly stuck in the ring groove . . . . but it went together ... and ran !

Being in the boring business for years, I've seen this exact same scenario before.
Backing up my theory, is the fact that the cylinder bore does not show any gouging like what would be found with a broken ring .... while running
Nor are there any pock marks on the dome of the piston from a broken piece of ring trashing about.

A new piston set and bore job will make it right . . . Just be sure and "chamfer" the upper and lower port edges after boring. 
Google "Chamfering Ports"  for more info

The other problem seems to be getting taken care of ....thanks to RT325 (and others) advice

As for the seals, yes, they might still be ok ... but since you have it apart, and since the seals are 50 years old at this point . . . . . . I'd recommend changing them out now as preventative maintenance.  Only reason not to would be if you can't afford it. 
Get and use original Yamaha double lip seals or their equivalent.
Using cheap single lip seals is like throwing your money to the wind.

 







. . . 
 

Well there ya go. Enduronut with many years of experience & a good set of eyes .
Very interesting & i'd say 100% correct.
Great explanation. Interesting what you can see with a good clear closeup pic too.

Impressive! Where I see some scratches and a chip, a whole saga unfolds before Enduronut. Thank you for the detailed breakdown, well worth a trip to the post office (even before the discounted piston).

Also appreciate everyone's input on the flywheel and seals - including RT's perspective on the woodruff key holding out. “You never know what worse luck your bad luck has saved you from.”

The cylinder is off at the machine shop accompanied by a 1st OS piston and I'm expecting a new pair of main seals on the doorstep any day now. From what I've read it's possible to replace both crank bearing seals without splitting the cases on this model bike, and a commonly suggested trick is running a long screw into a portion of the old seal in order to pry it out.

Does anyone have any experience using this method or advice on a different way to extract the current seals?

The screw method to remove the old seal can work, but I would not use a (long screw) or to mean do not screw the screw too far into the seal, the main bearing sits behind that seal and is a roller bearing with a metal cage that holds the balls in place, it is very easily damaged, if you use too long of a screw and damage the bearing cage then you will definitely be splitting the cases to change the main bearings.

Yes, as Lizeec says above, don't use long screws as bearing is behind.
I just flick then out on an angle with screwdriver, but not done it for a long time. Short screws & levering i guess although knowing my luck i'd drill a hole for the screw & the drill would escape through quicker than i could react then break off in the bearing. Just be careful.