Top alignment height for 39" cabinets is 93" from the finished floor. You use a laser level to find the high spot in the floor, measure from that, and draw a level line all the way around the room. It's the same with the base. You do a level line 34.5" from the high spot in the room, and shim all of the others to that level line.
With full overlay cabinets, you don't attach the molding directly to the box. You need an intermediate molding piece between the cabinets and the crown. You've got to have a cleat to attach to the cabinets, and then you attach the crown to the cleat. Take a plain 3" tall filler ripped to 1 1/2" and nail it together in an L shape. Apply it with the bottom of the L brought forward to the plane of the door, and the other section vertical. The cove molding is then attached to the vertical portion and touches the ceiling. That lets the cove "float" up and down the filler to account for any variation in ceiling height.
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