oh dear
Hopefully its just the piston,but i think having ground the hump out of the exhaust duct could have had some bearing on why that cylinder went 1st.
it probably needs different jetting for that cylinder as it wont run the same as an S straight exhaust duct.
I notice in your other posts you were changing the main and needle and going from 1 extreme to another (leanest to richest) on the needle setting,this will really confuse things for you.
Start with the main,go big and work down til it runs fairly well,double check the plugs to confirm it safe.
Then set the needle position,
start rich work down,again double check the plugs after accelerating through the gears.
Then when your happy its ok,double check the main,maybe go bigger just to confirm its safe,sometimes after getting the needle right you will find the main needs adjusting.
The choke check is what i use to confirm the needle is rich enough,i use plug reading and engine performance to set the main jet.
Keep it simple and work through it methodically,it takes time but it works.
Dont worry about the 1 piston,ive got a shelf load of pistons that have been sacrificed to the gods of speed
learn from the mistakes,in time you will be able to tell how anothers engine is running just by listening to them ride by.
You will find using a high quality oil will help prevent seizures,
silkolene pro 2 or motul 800 are very good ,some of the pump specific oils aren up to the demands of a tuned engine or high load for a long time (like a 3mile straight
).
HTH bud
Keep us up to date on the testing,and ditch that home made airfilter
ATB
dave
,bores look ok and head and ive got a spare piston 
