Wow, that's a lot of questions: Let me see if I can answer some of them at least:
Thickness - 3/8 is going to be pretty close. I will try and remember to measure them tonight or at lunch time. You don't have to have the exact same thickness, just close.
Where to purchase - I would start with a local machine shop, as they make a lot of parts out of aluminum, so should have some aluminum stock around. I buy a lot of my aluminum from the local scrap yard, as they have it segregated so I can spend five minutes looking through bins for anything that might be of use.
Holes - These are important, and must be right. You will have to measure your stock holes to make sure you get the right drill bit, and might need to purchase a drill bit from the local hardware store to have the right size. This is an important step, so worth the $10 on a new drill bit to be sure. As for your particular size, I'm not sure if Kawasaki changed the link bolts over the years, but my thought is that these have changed. To be sure, take off your bones and take them with you to the hardware store. Test fit the butt end of the drill bit into the holes until you find the right size. Don't try and use a tape measure...remember, this step is important.
Brass bushings - you can make the brass bushings easily enough by just using brass pipe from the local plumbing supply house. You will probably have to purchase pipe with the inside a little smaller than the bolt and then drill to fit after the bushing is installed. You will also need to purchase a second drill bit that is just smaller than the outside of the brass pipe to ensure you have a good press fit. The process is to slice off a section of brass pipe that is just thicker than the aluminum stock, press into the aluminum, and carefully file or sand the excess material from the inside of the aluminum. The first set you make should be without the brass inserts (if you choose to install), as they probably are not going to work anyway. If they do work, you can just redrill the holes for the brass inserts and press away.
How much lower - Well, that kind of depends. Are we talking about initial height change, or change with you in the saddle? For initial height change under the bikes own weight, you can check this by placing the bike on a stand with the rear wheel suspended. Take an initial measurement between the axle and the fender. Remove the bolt through the swing arm side of the dog bone. Support the rear well with blocks of wood or other material until the alignment on the dog bone hole is 1/2 inch offset. Remeasure your axle to fender and just do the math. If we are talking about difference under weight, this depends upon a lot of factors like correct spring rate for your weight; static and race sage settings; your riding position, etc. As a result, this is somewhat trial and error, which is why I think your first set of bones will be wrong, but send you in the right direction.
Well, how did I do for answers?
Rick