If you're using drywall screws, you'll want to countersink the holes. Drywall screws are flat-head, and need a countersink to seat solidly. If you're using Kreg pocket screws, the way I did, you won't want to counter-sink the holes. Kreg screws are pan-head, and seat just fine against a flat surface. Both drywall screws and Kreg pocket screws are self-threading, so you don't need pilot holes in the second sheet of MDF.
Building a Wooden Office Desk Organizer is an easy task for a professional woodworker, but not so much for normal people like you and me. But that doesn’t mean you cannot do this. Two years ago, I had almost no woodworking experience, but now I make most of my household and office wooden items by myself. This saves me a lot of money. And believe me when I say this; you can also manage to make wonderful wood items with a little practice and some woodworking experience.
In the Port Townsend School of Woodworking’s twelve-week Woodworking Foundation course, you will learn the essential skills, tools and mindsets of the traditional joiner. This is NOT an industrial arts course with a focus on machinery and production processes. Rather, it is a course in PRE-industrial artisanship--the creation of individual works through mostly hand tools and skills.. 
With the Grain: A Craftsman’s Guide to Understanding Wood by Christian Becksvoort. A little knowledge about trees goes a long way toward improving your woodworking. You don’t need a degree in dendrology to build a desk. But you do need intimate knowledge of how our raw material grows and – more importantly – how it responds to its environment after it has been cut and dried.
I really like this. I've been busy designing my own workbench to replace the ropey old thing I currently use. You've made me reconsider exactly what I need a bench for - I think I've been more than a little seduced by the idea of a beautiful hardwood bench when, if I'm honest, I don't need one. My cash would be better spend on timber for furniture projects that my family can enjoy rather than a wonderful workbench that I can only use on the weekends.

Once you start spreading glue, you have maybe five minutes to get the two panels mated, aligned, and clamped together. So make sure you have everything on-hand, and you're not gong to be interrupted. Start squeezing out the glue on one MDF panel, and spreading it around in a thin, even coating, making sure you leave no bare areas. Then do the same to the other MDF panel. Then pick up the bottom panel and flip it over onto the upper panel. Slide it around some to make sure the glue is spread evenly, then line up one corner and drive in a screw. Line up the opposite corner and drive in a screw there. Clamp all four corners to your flat surface, then start driving the rest of the screws, in a spiral pattern from the center.
Having done all this, I'm not sure I'd do it this way again. It might well be faster to layout the positions with compass and straightedge directly onto the top. Either way, you'll want to use a scribe rather than a pencil. Scribe lines are hard to see, and impossible to photograph, but the scribe and compass points click into them, allowing a precision that pencils simply cannot match.
The projects in this course follow a natural progression of skills, techniques and tools. Some of the early student-made tools are, in fact, used to help make the next tool or bench fixture in the series. You are supported in the building of these projects with step-by-step outlines, knock-down examples and continuing, one-on-one consultations with the faculty. Periodic evaluations of your progress with a specific faculty-mentor help keep you on track.
I mocked up the two scenarios, and determined that with the plate inside the stretcher the vise would have a reach of 8 inches, and with it outside the stretcher it would have a reach of 9 inches. I decided that 8 inches was enough, and that the extra inch wasn't worth the extra effort. With the end vise mounted like this, the right edge of the top would have no overhang.

@cahudson42 I bored the holes in my sandwich top with a 3/4" power auger bit with the drill in a portable drill guide that kept it vertical and in a way a bit like a plunge router. The guide screw of the auger was dead easy to centre over the laid out grid points. The holes are dead straight and clean sided. The auger bit was new which probably helped. As stated I have three rows from an end vise running the length of the front as well as from the front vise and holes in the front apron to support long pieces as well.
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Clamp the inner jaw of the end vise in position, leaving a little bit to trim off later, and then use the dowel and dowel center trick through the screw and guiide rod holes of the vise base plate to mark the position of the screw and guide rod holes in the jaw. Remove the jaw and drill 1-1/8" holes in the marked positions. I used the drill guide for most of the holes, and drilled freehand for the last bit. When you're starting a spade bit in a deep hole like this, start the drill very slowly, and the bit will move the drill into a perpendicular position. Start it too fast and the bit will bind and you'll damage the sides of the hole.
It might not be the easiest project in this list, but if you already have some experience with wood cutting and joinery, it won’t be any hassle at all. Thanks to the extremely detailed instructions it shouldn’t really be a problem even if you’re not very familiar with woodworking. This could actually be a great project for refining your woodworking skills as a beginner!
Anyway, I'd like to know if I'll be able to keep (EDIT: and use) all my tools out there (current and planned) without having the shed become a rust-bucket for the tools and machinery inside. I'll have a 10" contractor's saw out there along with a drill press, a sanding belt, a router & router table, and lots and lots of old tools that I inherited from my Granddad years ago. I live in the Seattle area, so it rains A LOT. But I'm hoping that with the proper ventilation I can keep the tools in the shed dry.
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