PG -
There are two basic budgets - R&D and Procurement (=production)
The production system is designed and planned under R&D. The production line itself is built, staffed and operated under procurement.
However, each year's procurement contract is self-contained and fully funded. The result is that the first year's unit cost (for two aircraft) was very high - and this is why it is silly and misleading to use that as the basis for "price cuts" in subsequent years.
So, as the production rate increases year over year, the unit cost should come down as less of the total is spent on building tooling and factories, and more of it on building aircraft (buying raw materials and parts and paying workers).
Another big factor driving down unit costs over time is that production engineers (who are there in large numbers to beat bugs out of the system) finish their jobs and go away.
However, it's odd that as we get into Lots 7 & 8 of the JSF program, with rates of 30+ aircraft a year (more than Gripen or Rafale, pretty close to F/A-18) the unit costs are budging by no more than a few per cent versus Lot 2.
You can compute a unit cost by rolling in a share of R&D, but it's not very helpful because (1) R&D has been sunk and (2) what share you assign to each aircraft depends on how many aircraft will be built, and we don't know that answer until 2030-something.