If the dealer installed the "factory" software for aftermarket pipes then your performance actually went down comparatively (against the gain from the pipes). The Triumph tune for pipes closes the secondaries a little more to richen the mix.
You will need to choose which way you want to go, PCIII or Tuneboy before you go any further. Both will get you where you want to go, but in different ways.
I'm a PCIII guy because it's plug and play as well as removable.
Tune boy is more involved, both in knowledge needed and invasion into the bikes software.
One of the tuneboy guys can tell you what they like in a package, I can give you what I like in a PCIII package.
What worked for me is PCIII, pipes, GiPro, triple filters and remove the secondaries. The premade PCIII software tune for this set up is "D&D's, K&N triple filters with secondaries removed". The brand names are unimportant, its the fact that its for performance exhaust, performance intake and without secondary throttle plates. If you choose later on to get a dyno tune, it's up to you ... a good tuner can tweek another few numbers by customizing the tune. The benefit to PCIII is that unplugging it returns the bike to factory settings should there be a problem.
According to Tuneboy guys, removing the secondaries and the GiPro are unnecessary with a Tuneboy, since they can be turned on and off with control over the software in the bikes computer. I do know that it's involved and some have difficulties with it, just depends how deep you want to meddle with the bikes software and how knowledgable you are about stuff like that. Done right, either way will get you what you want.
Your GiPro and secondaries question .... they are two different things, yes you should consider removing them with a GiPro. Secondaries control the throttle response and the GiPro controls the timing advance in the lower gears. The combination of the two is a fantastic power/throttle-response increase in low gears. It's like taking the training wheels off the engine.