A few things to try that could really help:
1) Bring your arm back more and keep your thumb and top of your forearm parrallel to the string you are slapping. This often solves the harmonics issue.
2) Loosen up your hand when slapping and let your thumb "bounce" off the string instead of doing a firm motion back and forth.
3) Often times you can get the clearest slap tone by using the side of your thumb's knuckle and hitting the string about 1/2-1 inch away from the end of the neck.
4) Rest the mid area of your forearm against the strings (particularly the (B) E A) just past the bridge to stop unwanted ringing and mute the the sound a little. This could solve much of the harmonics issue as well.
5) practice your technique a lot with very simple slap patterns until you get a clear tone.
I'm not the resident slapping expert, but I think that should help. Happy bassin'!
