Although it's hard to address everyone's feet, I'm not sure why running shoes shouldn't work for everyone. The important thing is finding shoes with a good fit for your feet. I have never worn boots when hiking, even when hiking with loads in the high 30 lb range. I have hiked in various cheapo New Balances, Montrail Hardrocks, and recently Inov-8 Terroc 330s.
If you are getting hot spots and blistes, where are they typically occuring? If they are on the heel, it could be a lacing issue, or perhaps you need different socks. At the start of my AT thru-hike last year I was wearing Montrail's with thin socks. I was getting constant hot spots on my heel, and I couldn't figure out why. I was lacing my shoes up tight to no avail. I finally came to find out that the problem was using socks that were too thin. By switching to thicker socks, all of the extra space in my shoes was taken away, and my heel had nowhere to move. Blisters solved.
Having said all of that, I think you should definitely keep looking into finding a way to use trail runners on the PCT. I would worry that carrying heavy, non-breathable books would wreak havok on your feet in the desert and wet High Sierra. I have fallen in love with the Inov-8 terroc's because of their narrow profile,but roomy toebox. These shoes are very breathable for the desert heat and to drain High Sierra water, have great traction, and fantastic underfoot protection when coupled with Superfeet insoles.