Rare? No. The turbo model was available in hard top up until '90 or '91 and while less common they weren't THAT uncommon. Another thing to check is if it's a swap or original... If originally a GTE the VIN will have MA71 in it; If not it'll have MA70.
No MKIII came with a 5 speed auto; They came with a 4 speed auto or a 5 speed manual... You're either counting wrong or the previous owner swapped something different in.
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