I had a similar situation and replaced the rubber damper, filter screen, fuel filter. I also had the injectors reconditioned (mr. injector) because I had been planning on doing that.
This is the thread i posted when I pulled the pump.
http://www.motobrick.com/index.php?topic=5576.msg35083#msg35083I followed Johnny's idea; removed the fuel pump and let it soak overnight in a glass container full of chevron techron. I wired the pump straight to the battery (I just held the wires against the ground bolt battery positive, nothing fancy); ran it backwards for less than 5 seconds then forward for a minute or two. It did not seem to pump violently as I expected. I had a hose loosely over the nipple and circled towards the bottom. No big blast of fluid. I thought maybe the pump had lost its power but put it back in and the bike has been fine since. It may not have been clogged with any black rubber bits to begin with. I saw nothing in the techron.
The bike did run better after all that. Before it ran similar to what you are describing. I say follow the gas and clean or replace what it flows through. If there is a good amount of black specks of rubber in the tank then some of it must have made its way through the pump, filter, fuel rail, injectors and fuel pressure regulator.
It all boils down to fuel, air, and electricity.
Replacing the ignition wires helped mine. Easy to check. On a dark night take the spark plug cover off and look for flashes while it is idling. Plugs ok? Valves in spec?
Vacuum leaks were another problem I had. The small rubber caps which go on the throttle body ports were cracked, the hose to the fuel pressure regulator (located in the 5th circle of hell), and the crankcase breather hose.
If wires / plugs are good, no vacuum leaks, and fuel pump/filter/injectors/regulator are solid, then the coup de grace is the throttle body sync. If that doesn't fix the issues then there is another level of fuel/air/electrics, but in my case those things helped significantly. Not perfect but much improved.
There are a few places to buy the damper/etc. This is where I purchased my things. No complaints.
http://www.euromotoelectrics.com/category-s/787.htmAlso, the small hose which connects to the filter screen was missing on mine. I needed to go to the dealer for it. Important b/c without it the screen is useless.
This was the soak. Then in a slightly bigger jar I wired it to the battery. I also poured the techron through a coffee filter and added it to a few tanks of gas.
