If your NOT EVER gonna go back then just cut and gut as u call it. I did this to my stock bio cube hood. I just gutted and cut EVERYTHING. Any holes left behind I just used aquarium safe silicone to seal them up. The stock splash guard I'm not sure about. Mine was smooth and clear not the diamond pattern you have. I would thing that diamond pattern MAY and I'm not 100% on this but it may send the lights in different directions other then where you intend them. I've looked into those lights and spoke with techs about them for my tank many many times but went a different route.
I would call them and ask them about the splash guard. Email the techs the picture, they will be able to let you know.
"When creating an aqua scape, strive for the beauty of imperfection, as its art and there is no wrong or right, it's left open for interpretation" James Findley