FUEL CONTROL HELP PLEASE !!!!!

Need some help with this "Tuneboy/Powercommander thing!

I purchased my bike back in October with only 1964 miles on her, 2006 standard. The previous owner had put on a Jardine exhaust and the Power Commander III. He had the bike dynoed and she ran very well, (dyno sheets showed 144 RWHP & 151 ft/lbs torque) with stock airfilter. I plan on doing my own thing with the intake and exhaust, and I have removed the secondary plates so I'm sure I'll need a new tune. My Question is; Can/ should I remove the PCIII and get the Tuneboy? Can/should they be used together? The PCIII is spliced into the main wiring harness (see white arrows on last two pidtures), and looks as if it might be a pain to remove. Also what is the small box with the green light on it? I didn't get any manual with it when I purchased the bike. I want to use the bike for some long distance riding, (Tahoe this summer I hope), and certianly don't want it to run lean on any cylinder. Assumming I use Tuneboy, (seems there is alot more flexibility there),how do I tell what changes to make and if they are effective? I know there are several posts concerning both Tuneboy and the PCIII. This is my first fuel injected bike and I don't want to make a big mistake and the engine suffer because of it.

Any Help would be appreciated and thanks in advance.

Lonnie

That green LED box is not a stock thing. Don't know if it belongs with the PCIII since I don't have one but my guess is it is a bike alarm module. Do you know where the wires hook into?

Far as PCIII and Tuneboy, you could use them together but I wouldn't recommend it unless you're careful to only do fuel map tweaks with the PCIII. If you don't plan on re-dynoing the bike then I'd go with Tuneboy exclusively and remove the PCIII. There are Captains with proper Tuneboy tunes for the setup you're looking into which you could use.

Otherwise if you want the custom dyno tune then I'd use the PCIII on top of Tuneboy for that unless you have a dyno shop that can tune using only Tuneboy - very rare.

I'm planning on installing PCIII just for dyno tuning, applying PCIII maps to the Tuneboy maps and then uninstall the PCIII until I need to go back to the dyno.

If you go Tuneboy and don't have a good knowledge of how to change mappings, then I wouldn't tweak fuel or ignition maps. Just use an existing tune from someone. Changing fuel mappings without a fuel sniffer to gauge the changes is iffy even for an experienced tuner.