To answer your questions in reverse order: 3) Install your floor coverings first. It will go faster and easier if you have no obstacles to work around. You can always cover the new floor with tarps if you need to paint, drywall, etc. in the future. 2) If you need to lower the height of the cabinets ,as you noted, the toe-kick can be sawed off so as to decrease the cabinets height by (+/-) 3 inches. If you need the height lowered further you will have to modify the cabinet carcass (think auto body chopping). 1) Laminate or wood? Completely discretionary. Whatever appeals to you. Laminate will take more abuse and more scratch resistant. Wood, on the other hand, is pure and elemental. Sealed with the right product wood will endure years before it needs to be re-sealed.