Hi Bushie, a bit of diesel, a thorough clean, blowout and a little oil around the bearings prior to assembly would be a good idea and definitely wont hurt.
As for the muffler i've never run a HC engine with the standard muffler, or vice versa but have heard of others who have and they claim they can't notice the difference. My only concern would be around having the right back pressure to help with pushing back the fuel rich emmisions for a "second" burn. Generally speaking these engines aren't too muffler sensitive and will run irrespectively but i'm unsure of the long term effects of that.