I'm thinking about picking up a 1999 GV with a blown motor for $1500 to replace my 1993 tracker with 230k.  I'm having an easier time finding lower mileage motors (2.5 L) for 2003-2004 model years.  I think the block is the same, but does anyone know if these later models are directly swappable without rewiring everything and changing the ECU?  Any other particulars to keep know when thinking about a swap?  Does auto/manual matter with these?

The only thing I can think of is a possibility that a sensor changed, and a corresponding change was made in the ECM.  This is sort-of backed up by the fact that the US parts manual lists a different ECM for each model year 99-04.

If you want to be safe, why not swap the sensors from the blown engine over to the replacement?

The ECM for the auto model is always different to the one for the manual model.

Hmmmm.... hopefully the wiring to the sensor is the same.  Another reason to get the newer motor would be to take advantage of the updated timing chain mechanism that the older motors were notorious for.