Order of operation - General considerations

Rule 1, do not remove any material that will later be used to hold the part
Rule 2, do every possible operation in a single setup that does not violate rule 1
Rule 3, if you do indeed perform the required operations out of order, struggle.

There is one other "option" that I can think of. That of making a "disposable" part early on to give you something to hold on to. I haven't looked closely at your object, don't have it in my hand to turn over and think about. But I have faced a similar problem in the past. Several times. A few for new construction, and several for grabbing ahold of an existing part for repair or fitting a new (or now standardized) part.

Normally I don't work to the tolerances that you have listed, but the same principals apply, just more time spent doing the fitting up. As long as it doesn't leak gas or liquid, that's good enough for me.