crazypete, that's funny about people thinking you had a turbo.
Mustang_289, once again looking at the harmonic balance, what kind do you have on there. I would check that first as that would be my biggest (most important) concern. Make sure the rubber is in good condition and it spins true.
When you say "vibration in gear at higher rpms" what exactly do you mean? Do you mean something like "in 4rth at 5000 rpm"? When you say "vibration" do you mean like Major vibration or more than you expected would be there? Do you mean it's vibrating througout the whole car or just a vibration you're feeling through tthe shifter? I just like to mention and search the easy and perhaps overlooked (but obvious) things first. For example, you will feel more vibration with the race short throw shifter than the stock due to the lack of all the rubber bushings and sound deadeners that are in the stock shifters. A little to moderate vibration in the shifter at say, yellow line rpms isn't abnormal in many cases. Also, as mentioned b4 you already have a new Al drive shaft (and new rear diff??).
BTW, how are you liking the Typhoon intake???