It will be more clear in a future FAQ, and I'll specifically list Programs this time around, since it wasn't entirely clear last time. But basically, any sort of item creation is supposed to be outside of the Missions parameters.
The main reason is that for 99% of the players, cost is one of the major balancing factors behind equipment. There's also currently no real restriction on down time for runners, now is there any requirements for a minimum lifestyle. This is deliberate, because no matter what limit we set on these things, there will always be a legitimate reason why Player X needs an extra week available for something.
In a home game, when runners want to take a lot of downtime, the GM can step in. Plots keep moving, story keeps churning. Things come up that can interrupt a lengthy downtime session. Maybe the GM turns item creation into part of the ongoing plot. Whatever, there are ways beyond simple time and money taht the GM can use to "Balance" out one character simply creating some/all of his core equipment. In Missions, you don't have that. And as the more, umm, creative members of the boards have shown in the past, it's all too easy to cheese out a lifestyle that requires very little money so that you can spend years doing things like programming max rating stuff.
Short answer: No, you can't build from scratch. There aren't enough rules to cover it, the rules that are there are often lacking, and there's just no way to put any real controls on it to make it fair in comparison to other players.
Bull