I don't know how you're set up, but if you can get your QD's so that one is male and one is female, then you just hook the QD's into each other. This also helps with hooking things up. You won't get things hooked up backwards if one is male and one is female.
This works for the hoses. As for the remotes on the tractor, I guess you're back to dust caps. The other option would be to get a short piece of hose with a male QD end and a female end and then use that short piece of hose connected between the out and in of the QD's on your tractor. Make sure the hose is long enough that the two ends of it can be hooked together to keep them clean too.
The chunk of hose with ends on it won't be cheap, but it will be cheaper than damage due to dirty hydraulics.