That's the combination I use ... PCIII, GiPro, TOR's, Triples and secondary plates removed.
It's all plug and play stuff you can do with minimum experience and tools, probably the least expensive (with the exception of PCIII vs TuneECM) route as well. With those mods done, a good dyno tune by an experienced Power Commander technician will bring it all together with excellent HP and Torque results.
The PCIII allows for fuel trim adjustments to be done by the tuner but doesn't allow for ECM editing on the secondary plates, timing or the 7% power reduction in 1st-3rd gears.
Removing the plates takes care of that issue and the GiPro restores the missing 7% with timing changes.
So to answer your GiPro question ... Yes, they work together very well. And as a bonus you get the gear position indicator. Simply adding a GiPro and removing the secondaries seems to be enough extra power for a lot of guys and they stop there. By doing just those two things, they are getting full power in all gears as well as smooth and instant throttle response without computer or fuel tuning necessary.
You can do everything I just covered with Tuneboy and TuneECM, but it takes more mechanical ability to get it right. It's a longer process to tune with them and very few dyno tuners will work with that system. It's much simpler to tune with a Power Commander module and dyno, takes far less time and is well supported in the industry.
It's also been suggested that using TuneECM along with the PCIII and GiPro works well. It allows for other changes to be made apart from tinkering with fuel/timing. I will be using TuneECM just so I can "look inside". I don't want to make any changes with it, everything is exactly the way I like it, it's reliable and VERY powerful. I couldn't be happier with the current set-up (but cams sound sooooo **** good

).