Wow, from everything you have described it sure does sound like fuel pump delivery volume. To me it does not sound electrical (coil, wires, plugs, ECM injector duty time etc). Measuring fuel pressure (yours is 60#) is important but a static fuel pump pressure reading tells you nothing about fuel volume or delivery capacity at 60 PSI. Something like a swollen O ring at the quick disconnect under the tank would restrict output flow without changing the static (or idle) fuel pump pressure at all.
I will assume the fuel tank sock is good & clean or was replaced. Fuel pumps are great "fuel pushers" and have very little ability to pull fuel. Any restriction on the suction side would kill its performance on delivery volume.
Another thing to keep in mind... On nearly ALL cages (Ford Chevy), each fuel injector has it's own micro-mini fuel screen right at the input of each injector. It is something that is never mentioned in any service manuals but they do clog and they ARE replaceable. I have never looked at HD injectors closely but I would bet they also have those screens, especially since the injectors are made by Delphi and I know that on Delphi automotive injectors, those screen are in-fact present.
Here is what those injector screens look like. They are easy to purchase and come right out using a sheet metal screw.
Fuel injector screens
Maybe others will chime in with some good suggestions. But based solely on what you said, it sure does sound like fuel delivery volume. I might focus on things like fuel inlet sock, restrictive quick disconnect below tank, micro screens in injectors etc. You never mentioned what the total miles on the bike was so I don't know how much wear & tear is on the fuel pump itself. You used the phase "for the last 35,00 miles" and that kinda hints to me that your bike has 75K or more on the clock. You also did not say if this problem came on suddenly or if it was a long gradual process.
That's important to know, because if it was sudden, it probably would not be the injector screens.
