Which income tax return form should I file?

Your PHD stipend is treated like a salary and it will be taxed accordingly as there is no provision to treat the stipend, intern salary differently than regular job. So your income through stipend in PHD, any other income that is attached can be filed through ITR- 1 form.

There are two more variations of this form but the default ITR-1 form is meant for the salaried employees. You can get the deduction for the Home loan of 8K from the tax filing. If your passive income and the active income through PHD stipend collectively stands from 2.5 to 5L then you'd be taxed 5%. Based on that you'd have to file the income through ITR-1 form. You can even file it yourself but it's better to read more on it or take help of CA.

You can read more about how ITR-1 applies to your case here : https://cleartax.in/itr1

I suggest taking help of CA to get a home loan to ensure better verification of rules and things, which we may often miss out, if we try ourselves. . Deduction related information is better known by them and to be processed through them.

It would be a good idea to get the help from a financial consultant, or better still CA for getting a proper information about the exact amount that would be taxable in your case. The income tax rules suggest that Wages, pension, gratuity, fees or commission or profits paid in lieu of the salary, advance salary, payment for leaves standing to the credit of the employee –all these form part of salary for the calculation of your taxable income. The scholarship earned for the cost of education is exempt from the payment of tax. From that point of view, your stipend remains to be taxable.
It depends upon whether your stipend is classified as salary or scholarship. If it is classified as scholarship, you can file your Income in ITR 1 and then claim returns. In any case, consult a Chartered Accountant for a better understanding.