1995 Toyota 4Runner transmission linkage too long after engine change.

This is a weird one. I have just finished installing a remanufactured engine in my 4Runner. No problems there, however when I went to install the shifter linkage it came up about an inch and a half too long. If I move the linkage to be able to bolt it up, my shifter shows as being in park but the transmission is actually in neutral. I pulled the shifter to inspect it and it looked undamaged. The interlock solenoid is working fine and I replaced the bushings while I had it out. Using a scrap piece of steel I made a test linkage that was short enough to correct the distance issue and the transmission and shifter were back to normal. Any ideas?