1) If your enetered the country in 2000, your F-1 status for the SPT ended on 31 Dec 2004. That means you met the Substantial Presence Test in 2005 and, you must file as a resident alien.
2) You file Form 1040, 1040A or 1040EZ. Do not mfile Form 8843.
3) The fact that you got paid by personal check does not change the fact that you earned this income and must pay income taxes on it. You should report the income earned from 1 Jan to 31 May 2005.
4) Yes, as a resident alien, you can claim these deductions.
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