It's called crappy synchronizers. Your 1st to 2nd gear synchronizer is the problem. The synchronizers in your tranny stops the internal gears from spinning when you push in the clutch so you can shift gears. When you are shifting at your 6000 rpms to seconds and it grinds it is because your synchronizer did not stop the spinning gears quick enough before you shifted and therefore you "ground the gears". This can be caused by a synchronizer not operating at 100% or your shifting, as in letting off of the clutch too quickly before you have it in gear and you hit spinning gears. The synchronizers, especially the 1-2 sychro, aren't noted as being very good in the T45 trannies in the 96-up GT's and Cobra's. Be careful. They will go out fairly quickly. Especially if you run the car hard alot or shift hard alot. Take it easy when shifting. Don't jerk the shifter into gear (this of course being for regular driving). Your synchro is the problem.
Now in Waldoo28's case it's most likely the clutch since it does it consistently in all gears.
The T45s in the GT and Cobra are similar but they are not the same. The gears and synchros as spinning very very fast at 6000 engine rpms. If the synchros are starting to go bad, especially the 1-2 synchro which seems to be the first to go in both transmissions, it will grind very easily at those rpms. Mine had to be rebuilt at 42000 miles and it hadn't been driven that hard at all.
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1996 Mustang GTS