Blackboat....I can hopefully key you in to some info about your bike. First...I have one!
A couple of things, that bike did NOT come with those cranks, they were not even made anymore when you frame was and if memory serves, I think it came with a full Ultegra 600 group back then. My very first road bike was the Tange built Ironman (yes, the purple and yellow one...lol) model just below the carbon, and it came with the first gen 105. I don't remember if a Dura-Ace bike was sold per se although I have seen DA builds on the road. As for the shaking when riding thing...I would caution a guess that it's a combination of things. Did you say that there WAS a flat spot in the wheel? That would add to it. Also, your headset may be loose and/or pitted and unless it's new is a pretty good possibility. Now, here is the part you can't fix...and it comes with a question. Does it "shimmy and shake" at any and all speeds? If yes, then it's most likely just the wheels, etc... If it only shakes at high speeds, like when your descending a hill, simply clamp your knees on the top-tube, that is simply due to the fact that that's a pretty big frame (58? 60?), and with an all aluminum fork, you may have a high-speed shimmy.
I was kinda bummed that your getting frustrated, in it's day, that was actually a pretty nice bike. I loved my steel one back in the day, and I like getting my "vintage" carbon Ironman down off the rack for a ride every now and again. I hope you get yours running well, I think once it's "up to snuff" you'll like it, but if not, there is actually still a market for them if you look around on the net.
Just a funny quip to end...my original Ironman (the purple and yellow) also happened to be my high school colors, so when I graduated, I sold it to my band teacher. He was a pretty avid rider and couldn't go without it.