Hi there. Nice to meet you. I have read all you have written down and I do have some feedback and advice. So first off will tell you some things I know about stones and crystals. There are so many different kinds. Each and everyone of us will and do react differently to the different ones. Each stone has a name and metaphysical properties in which it can benefit the user, but even though they all have certain benefits, some stones that work well for one person may very well have an opposite effect for another. So it's important to first find out which stones you are buying and using, read about there properties and then individually hold each stone, close your eyes and just feel. You should definitely get a sensation or/ feeling on how you feel and react to the particular stone. You will know if the stone makes you feel positive or negative, weaker or more stronger. Then we have the mixture of stones and crystals. Lots of them mesh well together and do help enhance each other's properties for the better good, but at the same token certain stones will not mesh well together and the person can have a loud overwhelming and not so pleasant experience with the group. So it's very important you listen to your stones and crystals and the way they make you feel. Experiment. You will know. You will feel. You will feel the positive or negative. Now it definitely is possible that some of the stones/crystals are making you have bad dreams and sleep and also it could be the mixture. Something very negative and sort of similar had happened to me before with one big stone I bought. After a week of bad things happening I felt could it be the stone and listened to my heart and intuition and got rid of it. I felt so much better after I did. Also it's very important to sage or in some way cleanse your stones/crystals after you buy them and bring them home! You want to delete and rid the stone and yourself from any negativity they may have picked up along the way before you bought them. Stones and crystals pick up energy quite like us empaths do. Also cleanse each one every couple of weeks or so forever after. The moonlight is a great way, burn sage through it and if you want more options then just research it. Next that brings me to the sage. Whoever told you that bad thing about using sage because your Navajo does not sound like that was a smart thing to say. Sage only is a purifier and cleanser and it only rids your home, yourself, stones/crystals from anything negative. Sage protects us and keeps us, our homes and stones/crystals safe. Very strong useful tool. Empaths should sage themselves often too to cleanse and rid off all bad energy/negativity picked up. I never heard anything like what you wrote down. Sage and Navajos should have nothing to do with one another except positivity! You can research it if you'd like but I can recall that many natives have used it to their benefit. I am part tai wa Native American too if that helps. There is another cleaning purifier to use called palo santo. It's a wood. They often sell it at places where you can buy sage. It also goes back to the ancient times as sage too with the same benefits. I personally though never liked it as much and the feelings I got weren't as pleasant. So stuck with my sage. But you can try it and it's used the same as sage. I personally prefer sage far more. Nothing bad will happen if you use the sage but do research on Navajos and sage first if it makes you feel better.Now lastly I'll talk about the dark thing you've been seeing. My moms house has dark shadows that go by sometimes but they are not in the shape as a human and some report those or an actual dark person in shape of a human. Regardless of what it is, we must ask them to leave. We must promote light and say prayers to whatever God you believe in and ask spirt that they go away and say this out loud and tell them in Gods name you must leave. The dark entity's are scared of the positive powerful light. Light always overpowers dark. Good overpowers evil. I personally believe in a universal God and believe God has no religion, like a famous monk also believes, but if you have a religion that's just fine too. A strong positive faith in something is important as long as the intentions are always good. SAGE is very very important too if your dealing with this type of energy around. So sage your entire house and as doing so you can also say "leave dark spirt or whatever you are, for you are not welcome here" and it sure will help! It may take a few times or more before they actually leave but it will if keep it up. By the way this could be energy brought in from a crystal or stone too so cleanse all of them then your house and yourself and see if that might just fix the problem.
Also stones can very well help aid us in many difficulties or just aid us by giving us extra help. Again research the stone or crystals then feel. Let yourself and intuition be your guide for which stone or stones work best for you. Read the name and metaphysical properties of each since all can be so different. A protective stone to have with you at all times is very important and especially for an empath! Black stones are most protective such as onyx and black tourmaline, but there are many others so research it and cleanse it often. Do the feel test and you will know which one works best for you. Also a rose quartz is a wonderful loving gentle stone that promotes so much love and goodness. I keep those in my purse all the time. Azurite stone is great for me. all the best vibes, love, health and happiness to you and your family!