I found a 1998 Geo tracker with the 1.6 16 valve motor. Will that fit in my 1988 samurai. The Geo tracker is obd 2. I want it to pass smog in the sate of California.

Yes, it will fit.
Not sure on passing smog in CA as an OBDII.
The smog machines read off of the computer as to it being OBDI or OBDII. I know you can take an OBDII engine and use an OBDI computer and it will smog check as an OBDI.
Not sure what all is involved, just know it can and has been done.

You might try calling a couple of the companies the make the conversion wiring harnesses such as Trail Tough or Petroworks...