Well, first off, make your crystal in photoshop/gimp/miscellaneous photo editing program, and save it with the same naming scheme as the other crystals. (I don't have KOTOR Tool installed ATM. But as an example, if the standard blue crystal is blahblah_001.tga, than you have to rename your crystal as blahblah_020.tga, or some other numeric under 255, IIRC)
After you save it, make your uti file. In the model variation field, put in the same number as your tga file (if you put in 20 for the tga file, put in 20 for the model variation)
For testing, make it so that it replaces an existing crystal. After you know the uti file and icon works, you can have it be a brand new crystal, without replacing the original crystals. I'm not sure ATM, as I can't exactly test it, but after you make your custom crystal, try to put it in a lightsaber, and see if it doesn't break your saber. If it doesn't, its ready for release. If not, you'll have to do some 2da editing. All you'd need to do is copy the row that you need, for whatever color, paste it, and replace the crystal name with your crystal's name.