If we took the rail runner from Sant Fe to the Zoo, would it be difficult getting from there to the train station using public transportation?

There is also bus transportation close to Zoo

If you take the railrunner to downtown albuquerque you'll arrive at the Alvarado Transportation Center. There are multiple bus routes that can take you all over the city. The 66 line travels up and down central avenue and I believe will get you close.

There is also bus transportation close to the Zoo

Check with the zoo as the trolley that goes between the two parks is down about 3 weeks ago. They might have information on this

Perhaps. I never rode the railrunner. I lived in Seattle for 20 years. However, you can do uber