Clutch/Tranny malfunction?

I recently purchased an 03 10th anniversary Cobra with just under 1000 miles when I picked it up. The car now has 2000 miles on it and I was wondering if anyone has encountered this problem. (car is stock except for a K&N airfilter and Pro 5.0 Shifter) While running through the gears I will powershift 1-2 then 2-3. When I go to powershift 3-4 it appears the clutch is not engaging completely if at all. If I let off the gas, push the clutch pedal back in and let it out in 4th gear the car will accelerate normally. The clutch itself appears to be in great shape and shows no signs of slipping. There is no clutch burning smell either. Any insight would be much appreciated.

Second Question, I believe my car has a build date of 7/03-would my car have the head upgrade that was supposed to solve the "tick"?

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