"Agency and W-2."
A Per Diem typically is not taxed. It should be listed that way on the W2. Backcalculate from the FICA, to prove what is being reported as Wages is not includes Per Diem. As long as that is paid under the terms of Federal Per Diem rate, of course.
The "stipend" is different; stipends from the employer are like shift differential. It's a bonus or increase in pay due to circumstances. It's treated the same as regular wages. Again, look at the W2.
What else did you want to report them as, and where?
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