There'll be a difference when you got to get tested for emissions and it says the vin is wrong.
I didn't put a 98 into my 97 BTW.
On the engine... overall it'* the same motor. The evap soleniods changed sightly but can be swapped over eaiily.
On the trans, you'd want to look into gear ratio etc.
We could do the swap with the wiring harness and pcm from the 98. There only one wire to move at the firewall. Other than that, it would come up on any scanners as a 98.
Column vs floor shifter isn't anything to be concerned with.. it all bolts to the trans the same way.
I'm usually available if you want a hand.