First, don't put any grease on the axle. Nothing should spin on it when assembled properly (ie, with all the spacers in place and the axle nut tightened properly). If you want you could put something like a rust preventative, but, I'd just wipe it clean and reinstall it.
Cleaning the old grease. I just kinda brush and wipe off all the old stuff as best I can. A popsicle stick and rag or paper towels will work. I usually scrape what I can with the sticks, then use paper towels for the rest. No solvent. You do not want ANY solvent getting to that bearing.
Exhaust collars. If you think you might damage one the next time then buy a spare. But, no need to change them each time. If you can use a lift for changing the tire then don't mess with the exhaust at all.
Some do remove the muffler anyway in order to use a torque wrench on the axle nut. I went by my Guzzi technique, explained by a good mechanic in Australia. Tighten it until red in the face, then add a bit more (his language was much more colorful). I use std length wrenches, not breaker bars. Just so you know, the axle nut is compressing the bearing spacers and the bearing inner races together on the axle. You want them very tight so nothing moves. Too tight won't hurt anything. Too loose might let things 'wiggle' in there, not good. About the only thing you could break would be to strip the threads on the axle nut. Don't think you can do that with 1ft long wrench and your arms
Oh, and make sure your bike is secure when tightening that nut