I think I've heard somewhere that kermit on the bike was a marionette puppet in the wide shots and a handpuppet in the closeups.
The shot with all the muppets on the bikes was done by connecting the bikes with rods. Remote controling the mouths and it was pulled in the front by some bigger bikes. And I think I saw an Interview with Jim where he told that one of the bikes in front where ridden by Brian.