There should be rubber boots and/or bellows that waterproof the cable ends. (see part picture) If they are missing, they should be replaced, but it sounds as if the cable is damaged and now needs replacing. You can slide the boots off, extend the cables, and lube the ends with marine grease, slide the boot back on and secure to the larger part of the cable with a small zip tie. This should help with water proofing.
On the throttle cable there are adjustment nuts and lock nuts. It sounds like the lock nut keeps coming loose, is not tightened, or the cable or nut is stripped.
It could be it is breaking inside, especially if it seems to be getting stiff.
I don't know what year that manual is for, but most, if not all of the basics should apply.
EVERY pivot point on both ski's should be lubed with marine grease once a year. This includes the stuff up under the cowel in the bow. If you can't get to it, at least try and spray them down with a good silicone lube.
How often are you flushing and rinsing the ski's with a salt neutralizing agent before treating with the t-9 ? Should be at the end of the day after every use. Spray everything down, inside and out, and since the stay at the water it needs to be eco friendly.
You guys can do most, if not all of your own maint. Just follow the service manual. I would suggest getting printed ones so you can mark the ness. pages with sticky tabs.