I don’t know which model you have exactly so I picked a random 25 EFI. They do things a little different than Yamaha so my info is not applicable about a filter inside the VST. It looks like they might have a separate HP filter, number 3 in the diagram. I still think the best way to test is with a fuel pressure gauge. There is usually a Shraeder valve someplace; but not always. Are you sure you don’t have some water in the fuel? The rapid decline in run quality that you describe is not usually consistent with a high pressure filter.
OK, well Bill’s diagram is helpful. Looks like there are a couple of different fuel filters in that system. And yes, just because the liquid appears clear in the filter does not mean it isn’t water. I would definitely drain it out and check…True, you would think there would be some separation of fuel/water in there, but perhaps not if it is all water.
It kinda sounds like the high pressure pump is crapping out slowly, but perhaps there is some other fuel delivery issue. Can you remove the plastic covers that shield the electric fuel pump? If so, I would try turning the key switch to “on” while holding fingers on the electric pump to see if it cycles on for a few seconds every time the key switch is turned on…
Look for the shrader valve like Bill says, must be there somewhere. You can probably “rent” the pressure gage from a local auto parts store to monitor the fuel pressure. But, beware, just cuz the fuel pressure might be low does not automatically condemn the electric pump….So, please don’t buy a new pump based soley on a low fuel pressure reading.