When you powdercoat the frame, or really any part of the bike, prep work is key. Masking off mating surfaces, bolt holes, or any space something goes through is a lifesaver.
I had my frame and engine powdercoated, and I spent at least 10 hours with a die grinder and dremel taking down all those surfaces. The places where the engine mounts was paramount because your bike will not work unless it's properly grounded.
When you replace bolts, be aware of galvanic corrosion. For example, stainless steel bolts into aluminum engine parts. Use anti-seize to prevent it. Also note that anti-seize acts as a lubricant and some say it affects torque so don't overtighten anything. The stainless steel is harder than the aluminum, so that's where you'll get your damage.
I don't know anything about the m-unit as it wasn't around when I started my project (otherwise I'd most certainly have one) but I've been seeing it on a lot of bikes on youtube and such.