LARoadster and all,
The replacement clutch link is for 1996 and newer Vipers with adjustable pedals only (this excludes '96 RT/10's). We looked at the linkage on the Gen 1 car and there's no practical way to lower the pedal, as the clutch master cylinder rod attaches directly to the pedal.
LARoadster, did you install the replacement link, or take a measurement of the one in your car (with it installed) and compare it to the one we sent you? Only if you took your stock one out and put it up against ours would you see the difference (I've been down this road before). Try putting the link in your car, it will drop the clutch pedal to the same, or near same, height as the brake, instead of being an inch and a quarter higher. If not, this will be a first. If you don't want your clutch pedal to be lower, send the link back for a refund or credit. It will only cost about $1 for US mail.
Regarding the shifting, I'll pass along the tip we used at the Justin Bell School when we had the Vipers. When you grab the shifter, point your elbow (as much as is comfortable) toward the passengers seat, then shift. Because of the seating position in the Viper, the drivers elbow is typically pointed toward his/her body, which causes you to shift at an angle, missing shifts. We used to go through this all the time on the first day of schools. Try it, it works.
Oh yeah, the shorter shift knobs and rods, as mentioned above, do work well in the Vipers. I have one in my GTS with a stock shifter.