twin 2005 300hp hpdi engines cut out

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

thanks
dan

Sorry to say, you need to empty the fuel tanks completely, Inspect the tanks for leaks, clean the vst's again and put in fresh fuel.

I will write this part in big letters.

THERE IS NO SHORT CUT TO CORRECT THIS!

Like Dockside said no short cuts. When a boat sits to long a list of things go wrong. A couple other things you might check that I found in the past are:
Your fuel tank vent lines . Could be restricted by bugs etc. Also you vent line may be clasped or bent.
Fuel tank check valve . Located at the tank where your fuel line connects to. it's a ball check valve that could be restricted. ( I removed mine years ago )
Also if you got a lot of water in your tank there is a SOCK that you put into your tank and it sucks up the water. I used it to see if tere was any water in my tank and I was lucky didn't find any. Sorry can't remember what the name was but it works great.
Good luck
flabob1