The issue with the older tracker/sidekicks and fuel injected samurais is internal to the ECU. when the mfg built the ECU's they used electrolytic capacitors on the circuit board. Over time these caps will leak an oil like substance and it will eat the traces on the pc board. haven't heard of that being an issue on the 99+ trackers but it wouldnt surprise me.
When this would happen it would knock out either the fuel injector or the pump circuit. but i have seen them knock out the ignition circuit too
best bet would be to try another ECU and see what you get. then its either junkyard or go over on zuwharrie.com. there used to be someone over there that repaired them. new last i checked were over $600.