Building a Goldberg Eagle II and just checking final fit and the rudder overhangs the stab a bit. Is it ok to notch the rudder to clear the elevator?

Yes; Trimming the rudder a bit on an Eagle will not hurt anything.

Hello!!!
bbbair is right, you would not use too much the rudder in your eagle
why don't you put a pic of your problem?

Have a nice day

Remember to allow clearence for full elevator deflection.