A high powered, high volume shop vac is your best fuckin friend.
Here's a pro tip. In between each run when draining the system to refill for a new set of plants, leave about 1/2" of water in each tote before vacuuming it all out and then wiping out THOROUGHLY with a CLEAN TOWEL, so that you can use a plastic wire bristly like brush to dip the brush in.
Clean the uniseals/bulkheads with the brush and use the brush to get inside the pipes best Ya can. Lucky for you, using the 2", Harbor Freight sells a 2 piece set that fits perfectly for the piping to clean the walls.
One more tip, you do want your bulkheads/uniseals low on the totes for obvious reasons, but it's really beneficial to leave maybe a 1/2" gap between the bottom of the tote and the bottom of the uniseals/bulkheads. Otherwise cleaning inbetween that tight space is a bitch. I have to use a towel edge pulled taught, to run through the slit to clean it. Wish my brush could just get in there.
You MUST CLEAN AFTER EVERY RUN!!!