Building durable customer owned tooling for use in production

I am wondering if anyone else out there has a good method for scheduling
that deals with...
1. Design Customer tool
a. Design
b. Ship and bill
2. Build Prototype tool
a. Build
b. Sample, ship and bill
3. Build Permanent tool
a. Build
b. Sample, ship and bill
4. Run production
a. setup
b. run parts
c. ship and bill

Each item is a line on the PO. Each item is required to be complete before
the next can start.
I would like the system, at the time of job entry, to schedule backwards
from the delivery date on 4, when to start 4 and therefore when to start 3,
when to start 2 and when to start 1.
Currently we do it by hand. I was thinking of adding 1 as a required sub
assembly of 2 and 2 of 3 and so forth. Only I have to ship each item to
bill, so they won't be available to be issued (and I would not want the cost
to follow anyway).
Does anyone have an elegant way of dealing with this.
Thanks,
Aaron Hoyt
Vantage Plastics