What year is your BF 225?
Do I understand correctly that your problems started just after you installed and external fuel/water separator? What make was the filter? Does it have a flow rate of at least 30 gallons per hour? Was it a 10 micron? If it has a screw wheel drain on the bottom, is that tight and correctly sealed? Have you tried bypassing it to test whether that is the source of your problem?
When you replaced the HP filter, did you also replace the LP filter? If not, I recommend that you do so. You might want to take another look at your HP filter. Make sure that the spring behind the filter is properly in place, that the flimsy little O ring is properly seated, and the bolts are torqued properly.
Does the problem start at a particular rpm?
If the primer bulb was getting really tight and "swelling" while running, that is really strange. I've never come across such a situation. Why not replace the primer bulb with a new one? They don't cost much. And that is a quick and easy way to check whether your LP fuel pump may be failing.
Take a piece of string cleaner mono and run it in and out of the vent on your fuel tank breather just to make sure it is not partially blocked.
I'm not sure that using an external fuel pump to suck fuel through the system is going to tell you much. The fuel pump on that engine is one powerful pump. A pin hole in the line or a connection that is not totally sound will pull air through the fuel system. Try the clear hose procedure.
I do not understand you statements "It seems like the vacuum makes the air bigger" and "Fuel flowed much better with no air at all." What do you mean by all of that?
If you do remove the VST carefully inspect the float valve for corrosion or scoring. It's possible it could be sticking. But if it sticks closed, it will cut off all the fuel to the engine.
I'm not familiar with the "filter" behind the intake manifold. There could be one there, but I've not come across it. I looked at the parts diagram for the intake manifold and did not see a filter. See link below.
http://www.boats.net/parts/search/Honda/Outboard Engine/2005/BF225A5 XA/INTAKE MANIFOLD/parts.html
There is a fuel filter screen under you HP fuel pump that can get clogged up. It's inside of part #29 in the link below.
http://www.boats.net/parts/search/H...06/BF225A6 XA/VAPOR SEPARATOR ASSY/parts.html
Last year Seachaser was having a fuel issue that he finally traced down to a fuel screen on the fuel pressure regulator. See thread and pictures in the link below.
http://www.marineengine.com/boat-fo...utboard-225HP-Engine-Light-quot-ON-quot/page2.