I haven't had to troubleshoot the fuel injection on a Rocket yet, and even though it is OBD II compatable, it has been simplified for use in this application and isn't real sophisticated.A lot of problems pop up without throwing a check engine light. Here are some thoughts...
Have them check the fuel pressure. It almost sounds like your complaint of bouncing off of the rev limiter could be a symptom of fuel starvation. The number three cylinder is the last one on the fuel rail and there may be very little fuel to work with after numbers one and two are done with the supply. The fuel sock in the gas tank may be plugged up with wood splinters (why would you do that?). That was a joke...
Failing that... I have no idea if the fuel injection is sequential, it very well may not be. That would mean that all three injectors fire at the same time, this is a very common setup in the automotive world. Whether it is or isn't, there is a little trick you can play. Disconnect injector number three and lay the plug to one side. Run a set of jumper wires from ingector number two's wiring harness to injector number three and try running number two and number three off of number two's pulse. If number three starts to work, I would look at the wiring harness for the injectors.
OK... now you made me get the shop manual out. Keeping in mind paragraph three above..All three injectors are fed a positive 12 volts from the ECM but each has a separate ground that is supplied by the ECM. The 12 volt positive feed wire is a single wire that comes out of the ECM and is SPLICED out to three separate feed wires, one to each injector. I hate splices. Test lights and noids are of little help here, you may be getting 12 volts in the number three feed wire but not enough amps to fire the injector. Sooo... if number three is now working with the jumper wires from number two but it won't work with its own connector try this...
Plug back in number three's connector. Run a jumper wire from number two's 12 volt feed to number three's 12 volt feed wire. If number three now works, you have a bad splice in the hot wire that feeds number three. If it doesn't work the power transistor in the ECM that switches on and off the ground may be fried. Before you condem the ECM you have to check that ground wire for continuity from the Number three injector to the ECM.
Also look very closely at connector number 21... the fuel injection subharness connector. I would unplug this and tweak all the pins in that. Connectors are notorious for having the little pins in them loose electrical contact and that could be killing both the power and ground to the injectors.
There also could be some sort of freaky problem like a chipped tooth on the crank that the crank sensor can no longer read for number three and wierd crap like that... but I really doubt it. Most of these problems are electrcal, I'd wager to say maybe as high as 95% of all fuel injection problems are wiring harness issues...
Your dealer may be frustrated because the Rocket is a limited production bike full of unknown electronics. One of his guys that has some electrical experience is just going to have to sort it out. If they have no one there that has an electrcal background you are in trouble..