97 GTX dies while riding.

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I am missing something here, I haven't found a smoking gun during this tear down. It was clear that the top end had been re-done and failed when I bought it, someone did some really crap work and either didn't address the original reason they had to rebuild it, or they caused the reason why the new top end failed when I got it. I clearly didn't find that reason either.
 
I have rebuilt the carbs, done the pop off tests and made sure they would hold pressure. I replaced the fuel lines because they were the gray tempo and also the selector because it was clogged but even having it bypassed, running straight from the filter it was still exhibiting the same symptoms.
 
I am taking a hard look at the crank case now, you can tell by looking at it that bolts have been removed since several of them no longer have paint and the last one on the PTO side for the balance shaft area was not tightened all the way. I am wondering if someone replaced only part of the case, like the bottom and it isn't sealing properly. On the PTO part of the crankshaft I did see some marks on the larger lobe that indicates to me that debris must have been made contact with it at some point, I will be looking into that further later.
 
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