I think your choice was the best way to go, getting a 'brand' new engine from a highly trusted "local" engine builder might be costing you but it will be a "once and done" deal where once that fresh 360 is in there you will never have to worry about it again.
Another point, when I got my 360 balanced at the machine shop I gave them a weighted B&M flex plate I got with a bunch of other parts; I got a call one day saying the balance on the flex plate was way off and wouldn't work with my 360, and later the machinist told me he figured out it was a plate for a 1973 cast-crank 340. Apparently the 1973 340 are balanced differently than 360s, at least according to my experience?