Pull-ups are for *inputs*. Clock sources are *outputs*.
I think there is some confusion... T0 and T1 are inputs (see section 14.3.3 of the datasheet). I probably should have said that I want to select them as the clock source.
And a base resistor connects between a pin and the base of a transistor. A pullup connects between the pin and Vcc. How that can replace a base resistor I'm not quite sure...
I want T0 or T1 to be held high while the transistor is off and pulled low when the transistor is on. The transistor in this case is a photo-interrupter.