By running the "new engine", do you mean running the engine while it's new (not broken in) or something else?
I am meaning, when your new engine is all broken in, has enough miles to get on it,, new.
Unless you get a handle on your A/F ratios in a safe zone (you have not done that yet, I will add),still too lean also you really need to know where your timing is are some of the ways your new engine is going to survive.
Sorry about your leg, your young & will heal fast.