You're altering your soil by removal of components and 'sample preparation'. Is this desirable? For what reason do you wish to undertake XRD and SEM on your soils? See also:
February 9th, 2012 Size and shape characterization in soils and sediments
the aim of your study is crucial, indeed. As you selected XRD and SEM, I suppose the mineralogical composition is given priority to texture. As far as the inorganic part is concerned you need to separate the various components such as light minerals and heavy minerals by heavy liquid separation after having split up the grain size. The finest particle size can be obtained using settling tubes. The sandy part can be shipped to the SEM-EDX/WDX lab and/or investigated by XRD using powdered samples. It would go beyond the current Q&A process to refer to the different ways of clay mineralogical analyses, applied to the clay fraction (see e.g. Weaver´s textbook).
If you want to study chemical and mineralogical changes in the course of soil formation you need to take oriented samples at outcrop and prepare slides of different size with the soil sample embedded into resin. Thereby you will get a full-blown picture of the soil or weathered material. The slides have to be scanned similar to your SEM-EDX/WDX, resulting in a full-blown picture as to the texture, quality and quantity of the mineralogy. For the identification of minerals you can use the electron-microprobe and/or micro-Raman.
I suspect that your selection of methods is mainly dictated by the availability of methods in your department accepting some limitations as to the dataset on the textural part. If you have access to one or the other methods mentioned in the last paragraph, you should sent at least some reference slides from each diagnostic horizon to a laboratory capable of handling them in the more advanced way described above.
For preparing XRD samples for clays, you have to consider minimizing the thickness of the clay sample down to 1 - 2 mm. Further, you have to polish the upper surface that will be subjected to X-rays. This would give you reasonable result because if you trim the surface without polishing it, you will end up with a surface that has a distorted orientations. What type of X-ray diffractometer are you using?
This question pertains to oriented XRD mounts prepared by decanation. After completing the ethylene glycol step and XRD scan, can I reuse this mount for the heat treatment steps? or do I need to have another oriented mount that was not subjected the ethylene glycol vapor?
For XRD we can have oriented mount and random powder. If you need oriented mounts you can use a filter of ~0.45 micron pore size and milipore along with a vaccum pump (see attached image). For random scan just place the clay powder in the holder and scan it for required scan speed.
For SEM you need carbon adhesive tape. Place it over stud. Now sprinkle the dried clay sample and using a fan or pump remove the extra clay particles. Now place the stud for Gold/Platinum coating and after that it is ready to observe under SEM.