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After being inside my 05 heritage, I would tend to doubt the theory about the holes in the hose unless anyone has personally witnessed them. I replaced mine with the one in the kit and let me tell you they are like iron as far as getting them on or off the pump/filter.
I don't recall if it was on this forum or not, but I have definitely seen pictures of hoses with holes in them. I had to get in my tank at 20k miles to replace the pressure regulator housing, and I could see on my hose where it was rubbing against the tank. It was very obvious and after another 20k miles it would definitely have rubbed a hole.
Check fuel pressure to rule out plugged filter or holes in tubing. If that pans out move into the electrics , checking all connections . Set up a good fan to cool engine and start wiggling stuff to see of you can get a reaction out of it with the bike running. Ron