For the tripod, if you haven't used one of those carbon fiber ones, it's a cool experience, but you'll figure it out quickly. Yes there are leveling plates available, mainly for panorama use. I don't use one since I don't shoot that many panoramas. It's not required for panoramas, it simply speeds things up. Without that plate, you will need to level the base plate by extending / collapsing the legs. You can certainly start without leveling plate and add one later if you need it. Just screw the ball head directly into the tripod base plate. For macro, yes you can use a focusing rail. I can surely believe you have spent days reading about this stuff, hehe! I didn't knew about a focusing rail when I started with macro! But just as with the leveling plate, you can start without it. Personally I don't use one. In fact, for macro, I don't use a tripod at all. It's too limiting for my use. I mount my lens on a monopod, which allows to follow the insect much more easily, allows to move closer easily, and allows to change the height much more quickly than with a tripod. Yet with some practice it's stable enough.
As for the DOF with long macro lenses, this is common misconception. When using long lenses at normal focusing distances, we all know that the DOF gets rapidly smaller as the focal length goes up, and with tele lenses the area of focus is very thin. But the simple formula to calculate DOF actually only works for non-macro distances. Once you get close to 1:1, the DOF almost exclusively depends on the magnification ratio and not on the focal length. In other words, if you were to shoot a subject at 1:1 magnification, the DOF with 100mm or 200mm would be almost identical. Why is this? With the longer lens, you would be farther away from the subject, which will cancel out the smaller DOF from the longer focal length. If you want to study the details, look up the DOF calculations on wikipedia. So that means there is no downside for a longer macro lens, except for the price tag and weight/size to carry into the field. And yes if you want the best, sure go for the Nikon 200/4.
I have also tried the 28/2.8 AIS. It is a bit sharper than the 28/3.5 in the center and shines at close focus distances. You can almost use it as a macro, works great for flowers and such! But here is the downside: At longer focus distances, i.e. for landscapes, the corners are rather soft. Even at f/8 or f/11 the corners don't get fully crisp. The 28/3.5 beats it in this respect. So primarily for landscapes, I can't recommend the 28/2.8 AIS. If you will be shooting it on the D800 and make big prints, you will notice the weak corners. If you can't get a hold of the 28/3.5, you can also check out the 35/2 AF-D which is very sharp across the frame when stopped down a little.