Well, if you want to go crazy, you take te entire thing apart, split the cases, and then scrub and clean out the engine with a solvent. I am sure you aren't comfortable with that, so the next best option is to flush it out. I will use mineral spirits. I fill up the crank case, swish it around, spin the crank, and basically just try to loosen all the trash inside the engine, and then I pour it out into a big bowl or bucket. Then if you want to not waste said mineral spirits you can pour it back into the container it came out of. Just make sure to put a coffee filter into the funnel. so you can strain out all the crap you just washed out of the engine and then the mineral spirits are good to go again.No i mean how do I clean out metal shavings? File them down? Dremel? Sandpaper? Do I need to be careful about overfiling. What grade sandpaper do I use
Some people will use 2 stroke premix gasoline to do this too. I don't because I like to take less risk with the whole flammable aspect of things, but it does work well.
I also clean the rings, piston, and cylinder.
Then just make sure to lubricate all of those same parts during assembly.