Thanks for the feedback, in the future Ill plan on the chimney flashing as well. Makes sense since masons in my area are hard to find. (Plumbers are a little easier to find, Electricians.... Shake a tree and five drop out).
On the job I just did, I ended up building a cricket behind the chimney and redoing the flashing around that part. Took me about 4hrs, including the material run. Choose to eat the cost, since I had not discussed it specifically with the customer (Not comfortable pointing out whats in the contract unless its significant). Also I did a lot of other work for the customer previously. Feel like a hack now, for not replacing all the flashing, next time Ill plan on doing it from the get go.
When I said "Base Flashing" I was referring to the step flashing and the pieces that go above the chimney and below. Everything except the Counter Flashing. I guess "Apron Flashing" might be the proper word. Base Flashing might be something I heard once, or maybe my own lingo. Thanks for everyones feedback.