1) Yes, you do have to file a 1065 for two partners.
2) Yes, technically you can file your 1065 on a fiscal year basis. But it really doesn't matter if you had done it on a calendar year basis. However, you may have to continue with this going forward.
3) You can still file on a calendar year basis and continue on that basis afterwards until you request a change from IRS. This might be more convenient than filing using a fiscal period. States levy most taxes such as property taxes in full based on the year of inception and is usually on a calendar year basis. So in short, it really doesn't matter whether you start with a calendar or fiscal period.
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