Sooo... I noticed after plugging on prime today that a couple of my 3"x25' hoses must have not gotten cleaned properly after the last use. My question of with they weat out the mud after a while or are they always going to be problem hoses? No big blockages or anything but rough on the sides.

Terry, try putting the dirty ones on the first couple hoses off the hopper, that is where the pressure is the highest and they will get scoured the most.  If they don't clean up after the first use or 2, then the next time do the same, only at the end of the job, just leave them on, Run the end back to the hopper, sugar the remaining mud and recirculate at a fairly good rate and let it scour.

Or else, leave them at home for a couple days in the sun, and beat on them with a sledge to break off the hardened layer around the inner circumference....or try both methods.... 

Try turn them inside out so the rough side is on the outside.. Works for my socks

No but.. My guess is that it should wear out quite quick..

Mud scaling in your hose isn't your problem Terry, mix design and a no water priming. Glad to hear your using your line pump its a sweet pump. Today i pumped up 140 stairs 7 stories 70 feet up, 100 feet of 2" and 100 ft 2.5", small gravel mix. No plugs 3d time doing this stair job. Mix design and a good primer is the key.