For myself, it took a little bit of time to get used to string skipping as well. I found that I made progress faster when I slowed WAY down, and practiced things very deliberately and controlled. I've only been doing this for about 3 weeks now, and I'm almost as good with the floating thumb as I am with the moveable-anchored thumb, which I've used for 12 years. The nice things is, there are no ringing strings.
I'm not Todd, but my opinion is that any due dilligence that you put into this method will pay itself off in huge dividends later. I suggest you get a metronome, slow things way, way down, and practice some of you runs while slowly working the tempo back up. Nothing makes things sound more muddy than a ringing B string, except a ringing B AND E string!
