Hi LongLive:
1. I think the problem you may experience with timing is (1) how long it takes for the USCIS office to process your application. Since you can choose the USCIS field office, you should choose wisely. Someone I know applied through New York under similar circumstances as you (had recently come overseas but already had a re-entry permit) had her application accepted and an interview within a few months. However, I applied 1 year and 4 months ago through Newark and still no interview; and (2) the fact that your contract is so short. If there is a high chance your contract will be renewed at the end of the year, then I would mention that and if possible also have your employer mention that in their letter, but add in your letter that you plan to come back to the United States within a certain timeframe (so it is clear that you do not plan to renew your contract and live overseas indefinitely).
2. Definitely file online. I filed by paper and it didnt help our case in any way. The abovementioned acquaintance applied online and her process was smooth and timely.
3. Send the money for the fingerprints but don't send any fingerprints. There is a high chance they will just re-use your wife's biometrics, but in our case we sent both the money for the biometrics, and also biometrics taken locally, and then we had a weird thing happen where the online portal said "biometrics appointment scheduled" but then no appointment was ever scheduled. When we called the hotline, the agent said on her end it said that we are "eligible to be scheduled for an interview" and no biometrics appointment is pending. So I think that us sending both caused some kind of confusion and human error on their side.
Good luck!