In column chromatography (microscale), after loading it with solvent and adsorbent and prior to loading the sample, what level should you allow the solvent to drop to? Why should you not allow the sample to run dry and what is the consequence if you had allowed it to do so? Why would water not be used to elute a column (besides it polarity) in column chromatography? When isolating separated compounds from a column chromatography, what would aid in the identification of compounds in fractions in the TLC analysis?

You should allow the solvent to drop to the level of the adsorvent, so it would never run dry.

When you let your sample to run dry it will never finish to flow from the adsorbent depending of it polarity.

Water should not be used because it can dissolve the adsorbent.

You could use another technique to identify the compound, as an infrared or a ultraviolet detector. You can also, if you know the compounds, identify it for the retention time, for example, if you need to detect two compounds, one more polar than the other, and use a polar adsorbent and a non-polar solvent, the first compound to exit the column will be the less polar one, because it will have a bigger interaction with the solvent than the stationary phase (adsorbent) and will go faster, the second will be the more polar one, because it will have a bigger interaction with the stationary phase.