Bad habits . . what are those?!

I think you are probably correct in it just being muscle-memory. I use EggBeaters and Looks so I always have to think about it when I first change from dirt to road or vice versa. Fortunately, I've been riding Looks since Greg made them so famous that my muscle memory issues are pretty minor.

Try clipping in lower in the stroke. Also, you may have to consciously pull up harder with your right foot to get the momentum going. You don't want to do it in a pack, but I may take 2 or 3 pulls with only the right foot if I'm really trying to get the momentum up before trying to clip in. Lastly, can you find a flat road without traffic (or a large parking lot) and just clip in and out, over and over and over, until you can do it without looking? This may help you develop that muscle memory faster. You could also practice this on a trainer, but since you are already comfortable with clipless pedals, it would be best to add the variability of the road.