Confirmed and fixed. The aftermarket pump was a pos and I sent it back. Got the oem one from iboats with a ten percent off coupon so it ended up about 170 shipped. It would have ran me at least 800 to have it done at the dealership.
Here's what I know now. The flow of fuel is pretty much what I stated above. When you click the first click on the key of a four stroke you should be able to hear the fuel pump whine if you aren't making too much noise. If it's not then either the fuel relay is dead or the fuel pump. On the yamaha f90 there are seven bolts you will have to undo, one of them is a sob that is located on the bottom of the intake manifold and you have to use a special tool to break it free. Then you will have to disconnect about 4 plugs and several gas/air/vent lines. It's not a big deal, it took me 2 hours the first time because I had to keep running to the manual or computer to figure things out. I can do it in 10 minutes flat now. After removing the intake manifold and carefully setting it on the side you have access to the VST. The high pressure pump is located in there. Remove it, if you order the oem yamaha pump then you won't have to mess with the wiring, I'd highly recommend that. The aftermarket one I had to remove the clips and that was a bitch as they are under the float. I ended up having to put back the regular oem one and then installing the oem fuel pump.
You have to prime the vst, to be sure I kept the lid off and filled it using the fuel primer bulb about three quarters full. Then I screwed on the vst lid and made sure that fuel primer bulb was hard. Then I clicked the firsdt key and kept the fuel line coming from the vst into a small container and sure enough the gas poured out meaning the fuel pump was running.
I buttoned it all up, put the mufffs on it and ran it several times, it fired up every single time. I'm not sure what killed that pump as I only had 500 hours on it, I have a feeling it was running the gas too low. Even though there are 3 filters before the vst somehow something must have gotten in there.