I'm just a very enthousiastic amateur, but would offer this as advice. I wouldn't worry too much about "muscle memory" as such, or be overly concerned that you're doing it "wrong".
Everyone does it wrong in the beginning. That's why I like the saying "practice makes perfect" and like very much less the saying "perfect practice makes perfect", as it's impossible to practice something perfectly if you can't do it yet.
In my humble opinion (again, as an overly enthousiastic guitar fan), don't worry about other chords if you're wanting to play a song with (say) D, G and A (or whatever). Learn those chords and the changes in the context of that particular song, and if you want to learn another song with different chords, learn those chords and changes in the context of that song. And keep doing that everytime you want to learn a new song. Don't worry about learning other chords when you play a D chord, worry about learning the D chord.
And (but once again, I'm an extremely keen amateur player with perhaps more motivation than talent), I agree that a lesson would maybe help put you on the track you want - it may help you to put together a practice scheme you'd have confidence in. If that's not possible, give yourself a little time and listen to what you're playing, keep trying to slowly make it more like you want to hear.
And I thought the guy in the link played just great and I can't play like that.
edit: wrote this while others were posting a response - the one by David Hilyard I agree with very much.
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