that's really a tough call, as you understand that it's not easy to troubleshoot an engine problem when it isn't in it's normal environment. Props to you though, glad to see someone not using a Chevy 350 for the swap! If i had to hazzard a guess it would be a fuel problem, you really need to verify pressure and if gas is getting there. Spark management would be my only other suggestion, but I really think it's fuel related.
you didn't mention too much about what you checked regarding if you're getting fuel...can you get a guage in there somehow. How are you feeding it? what type of pump are you using?
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'02 Explorer XLT 4.0L --Nice Vehicle
'97 Saturn SL1--Soon to be ditched for a Ford!
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