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According to this (dead link):

http://bitsavers.trailing-edge.com/pdf/nec/FD1035_Product_Description_Jul84.pdf

This is an archived copy of the FD1035 3.5" Floppy disk drive: Product Description July 1984 - PDF:

https://archive.org/details/bitsavers_necFD1035Pl84_876629

The outputs are open-collector, so a pull-up resistor is required. You can instead enable the Arduino internal pull-ups on those pins by

pinMode(indexPin, INPUT_PULLUP);
pinMode(track0Pin, INPUT_PULLUP);