If I read this right, all you're really looking for is the three K&N set up. All you would need for this are the filters that Pig9r mentioned and, for your purposes, I would go with the DynoJet Power Commander over the TuneBoy. You don't need to worry about the secondary butterflies.
I do not know if Triumph changed fuel mapping numbers with the Classic, but you will need the stock map loaded. On regular Rockets, it's the 20050 map. The Power Commander makes it's adjustments off of this map. It's pretty much plug and play. DynoJet has a map for Jardine aftermarket exhaust, that I believe would work with this set up as well. The Power Commander can then dyno tuned to your liking, if need be. I'm using their recommended map for my set up and it runs awesome.
The TuneBoy is great and offers many more adjustments than the Power Commander, and it allows you to alter the real fuel map as opposed to making adjustments down stream as the Power Commander does but is not as widely supported yet as the Power Commander.
Removing the secondaries gives you the 7% of power that Triumph takes away in the 1st three gears. Their purpose is not only to provide the "power reduction", but also to provide smooth on/off throttle transitions.
So, to sum it up, K&N RU-2780s or 1700s, which ever style you prefer, the K&N 62-1560, for the air temp sensor and a DynoJet PowerCommander and start with the "ms510-004 tune. This is my plan in the near future. If you are running the stock exhaust system, you may try a different map.
nullnull"canned DynoJet mappings"
Rain may also play a factor, there are water resistant covers avaialable.