Thanks to everyone for the advice.
This was my method of cleaning the gems.
1.) I got 2 glass bowls, small size, that were big enough fit the gems.
2.) Filled each bowl almost to the top with water (I ran the tap for like 5 - 10 mins to make sure it was okay)
3.) I put my hand over one bowl and asked father and mother, and creature of water to bless the water.
4.) I put a good amount of really coarse sea salt into my hand, and asked father and mother, and creature of salt to bless the salt
5.) I then put the salt in the bowl and stirred clockwise three times.
6.) Then I prayed to consecrate the water
7.) Then I placed the gems into the bowl, and so did my step-dad into his. The water covered the gems nicely, and I kind of stirred the salt gently onto the gems.
I am leaving them there for 24 hours at first, then re-doing the cleaning again, until the full moon comes into effect. The Amethyst chunk is like 5 inches by 5 inches, so I want to make sure it's 100% cleansed, and I might also bury it in the earth, and smudge it again. I think stacking cleansing never hurts. I see no harm with that.
After I feel 100% the cleansing is complete, then I can start to understand how to use energy to infuse the gems.
*NOTE* I was walking around yesterday, to the store last night, with the gems in the pockets, 61% waxing moon, and I felt like I was going to pass out, felt so energy drained. I didn't cleanse the gems other than smudging like I said in the OP, and no previous owner used these for the craft, that I know of. Would gems be able to drain your energy, if you are not properly grounded? or used to the size of the gems, or if they are not cleansed completely.
Thanks again everyone! :)