Danny Lipford Workbench Questions
I'll try to take your questions one-by-one.


You have two easy options for leveling the chalk line. The first would be to use a carpenter's level; you'd measure 34" from the floor at one end of the bench-to-be, then hold a long 2x4 to the studs with one end right at the mark. Lay your level on the top of the 2x4 and tip the 2x4's other (not at a mark) end slightly up or down until your level reads an accurate level. Now you can have a helper mark across all of your studs with a pencil instead of a chalk line. The second easy option doesn't concern itself with level at all, only with being parallel to the floor. Measure 34" from the floor at each end of your bench-to-be and mark that spot.
Since you're in Washington, I think you'll probably have 2x4s available in spruce or "pressure treated", and probably no other options. Spruce should be just fine.
The plywood braces (you can make them from either 3/4" CDX or ACX plywood) may be mounted only on one side of each stud or for greater strength &amp; rigidity may be mounted on both sides. I've built a "strongarm" wood-storage rack very similarly to what is described here; I used smaller braces, but mounted both sides. For most in-garage DIY purposes, a brace on only one side would be just fine. If you plan to do heavier work, you may certainly install one on the other side of each stud, too.
Elmer's Wood Glue, which is a yellow PVA (Polyvinyl Acetate) glue, is perfectly satisfactory. Franklin or Gorilla or TiteBond would also work just fine. You'll want a yellow glue or a polyurethane glue here; white glue gives you more work time before it sets up, but it's not as strong.
You could use nails instead of screws, but they'll be much harder to drive without damaging anything. Your siding is attached to the outsides of those studs, so every time you beat on the side of a stud the nails holding the siding in place will become looser. I'd much rather that you used screws. You can use 1-5/8" drywall screws. It helps if you have a drill to drive them (much easier on your wrists).
If you're not going all the way to the end, just stop wherever you want to stop. Until you install your benchtop, your new supports will feel very flimsy, but it will suddenly stiffen up when you install the top. There's no need for any additional brackets or supports.
Nope, the 2x4 braces don't have any direct attachment to the studs - they're held only by the plywood braces.
If you like, you could certainly stain and/or varnish your benchtop. If you do, though, and if you do any heavy work on its top, the stain/varnish will soon look terrible. You can use the same plywood for the top as you used for the braces. If you use ACX plywood , you'll have a much nicer benchtop than if you use CDX plywood, but a lot of very hard-working benchtops are made from CDX - they just have shallow knotholes in some spots (CDX may have "voids" and knotholes that won't be present in ACX).
I'd like to urge you not to make a 36"-deep bench. They seem handy in theory, but your back cannot be comfortable reaching that far - you get backaches very quickly. Really. I'm 6'2", and I'm not comfortable with any bench deeper than 24". Also be aware that a 36"-deep bench is going to work as a much larger lever against the wall, and so can't be expected to carry as much loading as a 24" bench can carry. If you're really sure you really want 36", though... make the triangular braces at least 24" square. That'll take quite a lot more plywood - you can get only (16) 24" braces from a full sheet, and your 36" top will consume a full sheet leaving you with a 12"-wide strip of "waste" that can't be used for braces.