There you have it. There are a few tell tale signs of the automatic.
#1 check the throttle body, there is a metal lever on the top where the kickdown cable would have attached. You'll notice the hook is there but no cable.
#2 The park safety switch wiring will be bypassed, you can see this under the shift boot. Look for some 'custom' wiring I think one wire is blue/white.
There are other ways to tell, various little bits here and there mounting holes, grommets, etc. But if the vin says automatic, then it was swapped.
Swaps aren't bad. But you'll want to check what kind of shift linkage/components you have before you buy anything.
Performance one step at a time.