1. Does this clause apply to each individual D.O. separately, or to the contract as a whole? Response: That depends on whether the contracting officer checked the second box in paragraph (f)(1) of the clause: "...for each order issued under the contract." 

2. Is it for labor only? Response: The clause could be clearer, as it uses the general term "service portion" rather than being more specific, i.e., "labor portion." Because the more general term is used, I think it should be interpreted as NOT for labor only. In other words, non-labor costs associated with performing the service would be included.