You clean the debris by splitting the cases. While youre in there (since youre having your top end ported) it would be a great idea to have your crank welded and checked out considering the extra stress you will be putting on it. How do you know the crank is good? Did you check it? If so, how? Porting the cylinders and doing a rebuild with a 13 year old crank is exactly my definition of half assing shit. Do what you want, it isn't my bike nor my money.