Crystals and Mica
The first crystal, Litherite, can easily be obtained by combining emeralds, ender pearls and quartz. This recipe is just a regular crafting recipe and can be viewed in JEI. There are several recipes associated with crafting litherite and you'll most likely want to aim for the one that uses 4 ender pearls, and 4 quartz in order to get the most out of your emeralds.
Eriodium, Kyronite, Pladium, Ionite and Aethium
All of these crystals have the same method to obtain them and that is through the Crystal Miner program in the Void Miner. In order to get the next tier of crystal though you will need to have the previous tier miner to mine them with.
Nanorite and Xerothium
These two crystals are obtained in the same way as the crystals above(through mining in the void Miner) the one exception being that your miner needs to be located in the End dimension.
You can however, mine these crystals in any dimension that you want but it will require you to craft an Interdimensional Modifier and replace one of your modifiers on your miner with it.
You can obtain mica using the Resource Miner(Multi Miners->Resource Miner) or the Rocky Resource Miner(Resource Miners->Rocky Resource) programs. Mica does not have a lens focus which means there is no lens type that will improve its mining rates. The best way to obtain it is using the Rocky Resource Miner program.