Form 1040-NR is the proper tax return for you to file in this case. While the same terms are used "resident alien" and "nonresident alien" they don't have the same meaning on the tax returns as they do in the immigration system.
For tax purposes you are still a nonresident alien.
Unless the immigration courts or your immigration attorney have requested that you file differently, this is the proper way for you to file until you meet the qualifications for the "substantial presence test".
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