Assuming you have your kit set up so that everything is within comfortable reach, I would start with your hand position. When I teach students, I often give them exercises out of Joe Morello's Master Studies. One of the biggest mistakes they make is starting with a hand position that is too high off the head. If you start with a low hand position, you can always raise stick height for accents or to move to a tom. This will keep the unaccented snare strokes at a low dynamic. Hope that helps!

I don't have much to add that hasn't already been said but I was doing these same type of excercises a few months ago (still practicing similar exercises from time to time).  I'll reiterate the "take it slow & use a metronome".  I also do quarter notes on the BD at the same time.  That should help develop the internal pulse. 

Again, think about keeping the sticks low on the snare and use bigger strokes & arm motion for the accents.  Make the toms pop.  I did a lot of work on the practice pad to develop the level lower stokes on the snare.