I'm going to try and be as descriptive and use as many key words as possible here. Again, just in case someone finds this using a search in the future....I know how frustrating it is to find threads with your exact problem, and then no resolution.
The bike is fixed, and holy hell does it fly.
I took off the tank (much easier than I expected) and replaced the fuel pump with the bosch one. It requires some modification, but nothing your average joe can't do. I cleaned out the mesh fuel filter while I was in there, and reassembled the bike. Including travel time (to and from my brothers, where I can work on things in a nice garage) it ended up taking 6 or so hours. Not really that bad, considering I wanted to go very slow and be meticulous. Fired the bike up, everything was good, no new leaks, squeaks or rattles. On the test ride, the bike still had the issue. It would fall flat on its face under hard throttle at around 7 thousand rpm (depending on throttle input, maybe 6000, maybe 8000) I was pretty upset.
The only other thing I could think of, was it must be the injectors. The 1340cc engine uses 2 sets of injectors. The primaries (larger ones on the bottom of the fuel rail) and then secondaries (smaller ones, top of the fuel rail) The secondaries come into play at higher RPMs and heavier throttle conditions. Since my bike is about 7 or 8 years old now, and only had 3500 miles, it's a pretty safe assumption that there was a lot of sitting around with gunked up gas clogging the injectors. Pair that with the fact that the bike needs not only to be ridden, but ridden hard to get gas flowing through the secondary injectors, and you've got a recipe for disaster.
So, the next day I rode the bike back to my brothers and tore the whole thing down again. This time, I also ripped off the airbox. This will expose the fuel rail and injectors. From this point, all you need to do is unscrew the four screws holding the fuel rail on, pull it back a little and you can unhook and take out all 4 secondary injectors.
Once you have the injectors out, you're going to need a few things: Carb cleaner in an aerosol can, assortment of heat shrink wrap and an assortment of tubing. Also, a 9 volt battery and 2 lengths of wire. Hook the wires up to each terminal on the battery (loop them around and hold them down with electrical tape (be sure the wires on each terminal aren't touching!))
Now, find some tubing that will fit onto the injector (the side that was plugged into the fuel rail) and zip tie it on, very snug. Using the assortment of tubing, slowly bring the size of the tube down until it is a close fit around the nozzle on the aerosol carb cleaner. Use heat shrink wrap at each transition in the tubes, so the are completely sealed.
Now that everything is set up, use the battery/wires to try and test fire the injector. Simply hold the corresponding wire to the corresponding prongs on the injector. You should hear it click. If it doesn't click, don't worry. Mine were clogged up so badly, I (my brother) had to drizzle carb cleaner through them and continually try to fire them. Eventually they freed up and began firing. Seriously, they were so clogged they couldn't even try to work when triggered.
This next part is tricky. You'll need to hook up your mutant tubing creation to your injector on one end, and the carb cleaner on the other. Position the injector so its in a cup or some sort of container. Now, spray the carb cleaner into the tubing, while using the battery and wires to trigger the injector to fire. Do this until it sprays carb cleaner through in a nice, uniform pattern. Try to fire the injector in short bursts, don't just hold it down. Once you've done this to all four, you're good to reassemble everything.
While you're in there, though, you may want to remove your secondary throttle plates. I did away with mine and I like the feel of the bike a bit more now.
I apologize if this isn't very descriptive. But search youtube for "Injector cleaning" and you'll be able to find videos that will fill in any gaps in my write up.
Again, if you're bike starts fine, the pump primes and everything, don't bother replacing it. If it has a high rpm hesitation, feels like it hits a wall anything like that, I urge you do just clean the injectors. You'll have to take them out if they're really bad, injector cleaner won't work worth a damn. Hopefully this ends up helping at least one person.