At 2 weeks old, kits should have plenty of fur of their own, so don’t worry about saving the mom’s fur. Changing the bedding would be a wise decision from a sanitation standpoint; if the bedding gets too dirty with the kits in there, they risk getting an eye infection. Since its going to be disgustingly cold this weekend, leaving a nestbox in the hutch will help keep them warm. Putting old towels or small blankets in the hutch help a lot, too. If its going to be below 20 F where you are, bringing the momma and babies in for the weekend would be a good idea.
Alfalfa has a really high protein % and should only be fed to growing kits and their moms. Normally, grass hay is better (which includes timothy).
Watch the mom for a little bit and see if she has gone in the box to feed the other kit. You can also tell the difference between a kit that has been fed and one that has not by looking at their tummies.