I usually just use some of that shelf liner stuff over the ends, strapped on with a rubber band or velcro.
Speaking of the S&S couplings, when assembled I try to keep the road crude out of the threads. Initially, I wrapped electrical tape over the ends of the S&S "nuts" but that was a hassle to get the tape wrapped well with cables in the way. Tape in the photo below.
But later I switched to sleeves of rubber cut from an old inner tube stretched over the ends of the S&S "nuts" as in the photo below.
That keeps the crud from the road out of the threads quite well.