- What are the good values for the pullup resistors?
The datasheet says that the outputs can sink 3 mA. 2K at 5V would be 2.5 mA so that would be a good minimum. Anything between there and 10K should be good.
- Is it possible to use a single resistor for both ports or does each one need its own resistor?
If you connect the outputs together you will get a logical OR of the two signals (the signal will go low if either output goes low). If that is what you want then you can use a single resistor for both.
- If JMP1 has both lines open, the INTA and INTB ports in the DS1337 wiill be getting some voltage from the arduino. Is that ok?
Yes. The chip doesn't care much if the outputs are used or not. It's just turning on a switch that connects the output to Ground. As long as you don't shove more than 3 mA into the outputs they will be fine.