twin 2005 300hp hpdi engines cut out

[dingo0722]

My twin 05 300hpdi just started to cut out. Yesterday we were cruising in heavy seas and started to notice that the engines would sputter at random at 3500rpm. Today we took the boat out and when we tried to open up the throttle it started to cut out right away.
This is a new boat to me. The boat was mothballed for 2 years. When I bought it I had all new filters installed, water separator, filter on the side of the engine and the VST filter.
When I removed the water separator today it was full of water on both engines as well as the filter on the side of the engine. I installed new sierra water separators filled them with fuel prior to installation. Took the boat back out again today and it still cuts out and died but would restart. The engines ran for at least 15 min putting through the harbor so I would think that all the air should be out. Any help as to what is going on here would be great

[Sequoiha]

most of the time when all the filters are changed there is 1 filter that is missed. it is a steel canister filter just above the VST, and your water seperator was full of water, and the engine filter was full of water then so is the VST, drain it,