After the mortar dries, go over the flooring with a fine- to medium-grit sandpaper with an orbital sander.
Put a dab of thinset in random spots that you can sand within 30 minutes. Clean up all the dust when you're done.
Protect the finished surfaces with masking tape first. Put the water-based adhesive in a roller pan. Start in the corners with a paintbrush, and be sure to use a cheap, disposable brush. Lay on a nice even coat, not too thick and cover the entire floor with a thin coat of glue. Use a foamed roller for large areas. Wait from 30 minutes to an hour for the glue to dry.
Work toward an open doorway so you don't get stuck in a corner.
Get a starting point, and the object is to have as many full tiles in a visible area as possible. Once the first tile is down, all the other tiles will fall into place accordingly. Use a laser beam to make laying cork tiles a work of precision since it shoots perfect 45-degree angles from the floor. Set the laser beam at the starting point -- where the edge of the first full row of tiles should go. Check your work by measuring from the walls to the laser line. If the walls are off, make adjustments to the starting line.
Lay the first tile in the corner, gently pressing it into place.
Be careful since adhesive is on the back of the tiles. It will be stuck for good once it's down on the adhesive and the floor.
Take a measurement and transfer it to the cork. Make the cut using a utility knife and straightedge. Don't worry about fitting tiles perfectly under any cabinets. A toekick under the cabinets will cover the edges as will the baseboard along the wall. Continue until the cork flooring is down.
Add a preset amount of catalyst to the urethane and stir for three minutes to activate the chemical. Pour a small amount on the floor. Use a synthetic fleece applicator, and go in one direction to avoid streaks.
Tip: Hold the applicator like a snowplow, so liquid will be pushed away from the area you just did. And use slow, smooth strokes to avoid bubbles.
Take a measurement first, and use a power miter saw to cut the baseboard so it fits into the corner. Nail the baseboard into the stud with a finish nailer. Putty the nail holes when you're done.
Measure the length of each cabinet and cut the toekick to size.
For an unfinished edge, use strips of wood veneer and measure a piece that's a little longer. Cut it with a utility knife and line up the edge with the finished grain of wood. Set an iron on medium heat to activate the hot-melt adhesive (it will harden almost immediately), and set the piece upside down. Trim off the excess with a utility knife.
When nailing in the toekick, press it up against the cabinet since the shoe will hide any gaps against the floor. Apply the shoe.