There are two separate issues that are often called "wobble". First there is the understandable front end shake caused by the handlebar mounted batwing fairing. Any windshield or fairing mounted directly to the bars is going to affect handling, it's something you eventually get used to. As noted earlier in this thread, recognize it for what it is, relax, and give the bike it's head. The worst thing you can do is put the death grip on the bars and fight it.
The second issue is what I consider to be the real "wobble", and that is the failure of the rear wheel to track perfectly true with the front due to side loads distorting the rubber mounts. Swing arm and frame flex are involved also, but the biggie is still the rubber mount system. If you ride behind someone with a severe case of the wobbles, you can actually see the rear tire walking around. Definitely spooky. This is the phenomenon that the Sta-Bo bushings and the various stabilizers like True Track and Ride Str8 are supposed to help. It is also the one that Dan's original question is concerned with, ie. does the relocation of the upper engine stabilizer link from between the two heads under the fuel tank to the front head and frame downtube make any difference in this type of wobble? I personally doubt it, but a point was made in a previous discussion of this topic that the frame would likely be stiffer where the link is attached now, versus the old backbone location. So possibly you would have less drivetrain movement due to frame flex. Of course, you still have the same rubber bushing design at the trans mount/swingarm pivot, so IMHO you will still get side movement under side loads.
Jerry