Im not sure if the newer trackers have problems with ecms like the older ones, but the symptoms sound the same.
We put a 1993 tracker motor in my freinds samurai. It ran great for a few months, then started missing and had no power. Finally it would not start at all.
Suspected no fuel, there was no spark.
We put a new coil, dist pick up, and the ignitor box that bolts onto the coil bracket. We had all these parts in stock, but nothing changed.
We grabbed a new used ecm from a freinds tracker and it fired right up and runs better then ever. After a littlle research it seems like a common problem with trackers.