Duke I have concerns about the dobek insomuch as getting help here later on. Myself and many others here are familiar with the PCIII and can help you set it up and get canned tunes or copies of dyno'd bikes. Your aid availability is seriously hampered in the case of the dobek, there aren't any "tunes" that can be loaded to finish the install or even to use as a starting point. It's up to you if you want to try and adjust the fuel by ear and save a few bucks, I do know that the PCIII combination I told you about got me the same dyno results Dougl mentioned above with the tuneboy and same mods as mine, so there isn't any power advantages either way in tuneboy vs PCIII, I couldn't tell you what to expect out of the dobek. Skip likes it, I'd love to see how it does on a dyno to compare results.
You are right to not remove the secondaries or install the triples until you have a way to adjust the mix, doing those in combination is the best way.
Don't concern yourself about the triumph tune, I'm sure it's fine and can be tweeked later on with either the PCIII or dobek, once the secondaries are removed it won't matter.
You might want to decide which way you are going to install the triple K&N's, whether you are going to slap a filter/cover over the temperature probe or install it back into the airflow by putting a hole in #1 K&N so that it can properly read the intake temps. If you go that way you will only need one small filter for the crank case vent. Deciding in advance will save you spending money on a second little filter and give you the chance to make a short extension for it's wiring harness.
Whatever you decide to do, I'm sure there will be someone here willing to help if you get stumped, so don't worry yourself any until the big day arrives where the parts start flying. LOL