I'm assuming your BF 250A has the same fuel system as my 2007 BF 225.
Based on the information you gave about the messed our HP fuel filter, I would do two things right off - drain the VST (instructions should be in your owner's manual) and, assuming that you have an external fuel/water separator (e.g. Racor) change it. When draining the VST, get it all out. The last parts are slow. If necessary, turn on your key switch for a few seconds to put more pressure on the system.
Take the boat out on the water. If it starts bogging down, open the cap on your fuel tank filler tube. If that helps, the vent to your fuel tank is clogged up. Run a long piece of weed wacker string down through the vent tube. If still bogging down, have someone feel the primer bulb to see if it is partly collapsed. If so, the fuel pick-up screen in your fuel tank may be clogged up, OR the check valve in the primer bulb may have failed. If primer bulb is not partially collapsed, have someone rapidly squeeze it. If that helps performance, you may have a failing low pressure fuel pump. OR, you may have a fuel line restriction between the primer bulb and the on-board fuel-water separator. Check the fuel line closely. Remove the plate where the fuel line and control cables enter the engine. The fuel line will often get restricted where it enters behind that big black grommet.
If still a problem, bypass the fuel line from the low-pressure filter and the low-pressure fuel pump with a clear plastic tube of about the same diameter. Run the engine until it bogs down and have someone look for air bubbles in the clear plastic line. If so, you have an air leak in the fuel line or fuel line connectors. At the same time, observe the fuel level in the low-pressure fuel filter bowl. It should stay at least half full.
If none of this helps, come back at us.