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It's possible you are having a turbo issue. Have you pulled the filter off and turned the compressor wheel after it acts up? It should turn very easy and not have any resistance.
I don't think a wetstack condition would cause the issue you are having. Is it slobbering oil out the exhaust...
I don't not work for a dealer but I do maintain a fleet of tender boats with these engines. I buy parts from our local John Deere dealer.
I have the John Deere Service Advisor diagnostic program if anyone needs any info.
Can you provide a serial number by Private Message? I work on these 6068's daily.
Is this High Pressure Common Rail?
ETA: I just read your second post saying it's not an epa unit.
I know you said MEP-016B, but is it a MEP-016D? I didn't know the B model had a glass bowl. If I'm wrong I apologize.
This is the fuel valve on one of my MEP-016D's. It's set to pump from the belly(bottom) tank into to running(top) tank.
I know you said 12v, but I used one of these along with two 12v batteries and it works fine. He's also a member here.
http://www.lakeserv.net/mep/dc_regulator/index.html
Can you push in lightly on the white part in center of pump?
My pumps don't look like that. Mine has a twist off cap on the bottoms. I THINK that visible part mat be a check valve? Maybe it's stuck? Just spit balling here.