The way to avoid any problems is to talk to the driveline shop that will do the work. They'll tell you where and how to measure. Most shops do not measure like the FFR Manual, they go from centerline of the u-joint to centerline. My shop had me bottom out the input into the trans, then pull it out 1" before I measured.
I agree with CEMI, just a word of cation. Do not go over the 1" that the tell you. reson is that the rear end in the cobra dose not have that much travel and the longer the drive shaft the less chance of binding you will have, if I did it over I probably would only go with 3/4".
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