My speedo drive on the 1.8 was leaking and squirrly loose. I took a working drive off of another 1.8 motor, put on a new seal, changed the gear oil with new Swepco, and now I'm having trouble shifting. It's like the shift linkage and the tranny are in the wrong position but I didn't change anything else.

Before it was siilky smooth. The speedo drive pushed in ok and the lock bolt fit right into the hole properly.

Can the drive be installed in the wrong positions somehow?

No This seems like a shift linkage issue that has happened as the same time as your seal.