It can take plaquenil between 3-6 months to fully work. You may actually get discouraged thinking it isn't doing anything but it is, it is just slow. Most of the side effects you mentioned can be helped if you make sure to take it with food.
As for the MCTD, I know it is scary but in a lot of ways it isn't much different than getting a Lupus or other AI diagnosis. Once you get diagnosed with something they often times find that you have other AI diseases as well. We call it "overlapping" diseases. Lupus often cause issues with the skin and you need to make sure to limit your sun exposure/UV Rays (wear sunscreen and hats if possible when you are in them) and also watch what lotions and things you use. I know I have to be very careful of those because they cause skin issues for me.
Try not to "borrow trouble" as my mom would say. Don't panic over the future. Most AI diseases are not death sentences and once you get them under control a couple of maintenance medicines a day will be a breeze