To clarify, I do my muscle memory exercises, give my hand a 5 minute rest, and then start working on the chord progressions using a metronome. I usually do some no tempo work first just to get my head in the game and then start stumming to the metronome, starting REALLY slow and increasing by 2-5 bpm as I get comfortable with the current speed. Most of the chord changes I've worked on I can get up to 60 bpm within a week or so.
Being an extreme newbie myself, I was really impressed at how this muscle memory exercise helped.