2004 BF 225 hesitation and bog at low RPMs

First noticed the engine stutter or shake at idle on the way to ramp a while back. Flushed at home with no issues. A few weeks later ran offshore no issues. Fast forward to last weekend, started engine at home before setting off, no problem. At the ramp, first turn of the key, 1 rotation and nothing, like the batteries were dead. fooled with battery switch and engine started. left dock and noticed stuttering or shaking again. went to take off and motor bogged for a while. I checked primer ball and it was full, tried to plain again and motor bogged for about 30 seconds and then kicked in and jumped on plane and ran fine at top end. Anytime we stopped the same happened, bogging for about 30n seconds then takes off to WOT no problem. Back at home I noticed much more carbon or soot at exhaust. Any thoughts? I pulled the intake manifold to test the fuel lift pump since the oil looks thin and thought maybe it was allowing fuel into the block but no fuel leak there. I did find about 3 cups of water drained from intake manifold when I removed cover. Any thoughts on how the water got into the manifold and or why motor is bogging on takeoff? Also, is there a way to test the fuel pumps?

Smell the oil for any smell of gasoline.

On the cover to the HP fuel filter, there is a bolt for fuel pressure relief. Insert your fuel pressure gauge there. You will need a 6mm adapter. Warm engine, at idle, fuel pressure should read 41 - 48 PSI with vacuum hose removed from fuel pressure regulator and clamped or plugged shut.

Also, on the fuel pressure regulator there is a fuel return line. Make sure that is not clogged or kinked.

I don't know of a good test for the LP fuel pump except to remove it and make sure that the plunger is operating correctly and not too stiff.

BTW - when was the last time you changed the HP fuel filter. These engines are very sensitive to a clogged HP fuel filter.

boat and motor is relatively new to me. I'll add this filter to the list of parts I'm gathering. Lots of rusted screws and bolts found under the intake manifold so while chasing issue, i'm attempting to pull and replace them. When I got the boat the gasket for the cowling was shot and i replaced it but did not realize the damage done. Doing some proactive maintenance while troubleshooting. Also going to attempt to clean the VST while in there. These are some of the worse rusted bolts. I've been applying penetration oil daily and hope to get wire brushes on them before attempting to break loose. Wish me luck!

Water should not be in the intake at all. Have you checked your sparkplugs, this sounds horribly like a corrosion leak into one of the cylinders that is small enough to clear at higher rpm?

wouldn't there be water in the oil if this were the case?

Not necessarily, you asked how water can get into the intake, the only way is if the motor has sat tilted up in rain without the cowl on, orherwise water has to have come from inside the intake. If you remove the spark plugs and check for a rusted electrode you will soon know what's happening.