The problem lies in the HD head unit, it's setup with an EQ curve that is designed to work with the Boom stuff. Other low power amps don't really have an issue with this but as soon as you put real power to it, it's distortion city and sounds like a bag of beaten cats.
The best thing you can do it gut the whole things top to bottom.
It all comes down to how much is your budget. There are a ton of setups and range from as little as $350 US, the sky's the limit though.
I decided to keep my 6.5 Infotainment head unit but I may dump that in the future too... it's a shame because the idea is fantastic with huge screen and GPS, it's the only waterproof option with a double din screen... currently
I started off with a Cerwin Vega B2 and a set of Inifinity Kappa 62.11i's and a Biketronics Line Leveler (the LL helps with that EQ curve I talked about). That system was fine and blows away any Boom setup even with only 2 speakers!
Unfortunately I wanted more lol I am now running a Rockford Fosgate TM400x4ad with Arc Moto 602's and the sound is night and day different. I'll post a couple of videos at the end of this post so you can compare, you can also browse through my channel and see the different combos I've done so far.
I'm still going though, I have a set of Biketronic Titan II's that will be going in the lowers (when they arrive) and I also have a set of Arc Moto 6.2's that I'll be putting in. I'll only be running 4 speakers, just not sure which 4 yet
I really wish the MOCO stuff were better, especially for the price you pay for it, but the reality is it's just crap
Biketronics offers a RG specific kit, maybe you could sell off the Boom stuff and get it or piece together something.
Good luck my friend, I hope you can find some sort of audio bliss