Measure your anticipated location for your built-in desk. Alter the measurement for any trim, mop boards or chair rails you plan to leave in place.
Order drawers from the kitchen department of your local home improvement store. Come with measurements in hand. Ask for the installment set that usually comes with drawers. It should contain some specialty screws.
Request a counter top per your measurements. Keep in mind your home's color scheme. Ask the store to end-cap both ends and to cut off the back-splash section of your counter top.
Stain and varnish your drawers. Allow to dry for at least 24 hours.
Assemble the desk by bolting the drawers/cabinet to the wall. If you have trim, you will need to remove it or cut it to make the drawers/cabinet fit flush to the wall.
Cut the 2-by-4 to fit your nook area beside your cabinet/drawers, and nail it to the wall beside for a support for your counter top. It will need to be level with the cabinet/drawers for the counter top to be placed on top of it.
Place your counter top on top of the 2-by-4 and your cabinet/drawers and bolt your counter top to your drawers, the 2-by-4 and the wall. Aim for studs, as your counter top has quite a bit of weight.