Currently prepping a Malossi 166 kit to slap on pnp to start this summer. First time doing this. I chamfered the ports and already made a mistake by slipping and nicking the cylinder wall. DAMMIT! Other than that I was pretty steady and smooth with the dremel. Should have stuck with the hand file for the small transfer ports because they are hard to reach. The scratches did not seem very deep so I figured I would attempt to fix it.
I decided to try to salvage the nicks by using polishing cream and a buffing bit on the dremel. That only shined it up, didn't remove the nicks, so I then sanded them out 1000 grit and then re-honed the bore. I think it looks good and hopefully this does not ruin compression or cause any issues. If this is wrong.. feel free to criticize me. I am just going full speed ahead and learning from mistakes as they happen.
Next is to sand the head and cylinder top absolute flat.
Using FMP notes, I am gonna try to hit these timing points using base gasket/head gasket and shaping the exhaust port to hit desired mark:
Exhaust time: 176 degrees
Transfer time: 120 degrees
Blowdown: 28 degrees
Other upgrades acquired and waiting to be installed:
22T clutch upgear
dellorto SIP 24/24 Carb
Once I get it set up and running good, I'll leave it like this until next winter when I rebuild the engine, replace the crank and match the cases if it does not provide enough as is.

two nicks right on the bridge between transfer ports. This is after polishing cream/buff wheel.

all the buffing wheel did was make the nicks shiny and smooth.

tiny sandpaper slices with a twitchy finger.

re-honed with a cheap ass harbor freight tool.