A new cylinder is just that. A new cylinder, which is a part that gets 'broken in' during break in. It's not a good idea to mix a new cylinder with old piston rings. Change both together.
As far as your oil mix ratio, 40:1 is just a little shy on the oil side unless the oil you're using is formulated to run at that ratio. Some guys do run 40:1, even with standard 2 stroke oil but I'd stay with a 32:1 mix with regular 2 stroke oil. Whatever you do DO NOT RUN 16:1. Too much oil even during break in.
Just a word or caution; The aluminum intake manifolds don't have a lot of meat so go easy on the grinding. They are also prone to breaking. I'd go with a steel intake if you can get one.
Tom