Hello Austin,
no ignorant at all your questions are absolutely appropriate!
Here're the answers:
1) Yes, all the systems are modelled: some of them are simulated at 100% (such TCAS) and some not (who do really need the maintenance page of the MCDU?), this because technical and/or practical reasons
2) Wx and terrain radar is under development and I've yet to decide which radar I'll implement (I'm testing various possibilities, wrong implementation means big frame rate impact and I want to avoid that), that's the reason you don't see it between the MCDUs
3) No, the alternate gear extension is not modelled, it could be added in a future update but it will not be in v1.0.
We too hope to have it ready soon, believe me!