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1996 3.5 interrupt sport engine firing or computer?

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My mum has a 1996 interrupt, and said there was something going on with her car so my dad fixed that problem but now it's firing wrong, my dad says cylinder 1,3, and 5 have erratic spark and her check engine light stays on even tho we reprogrammed it. My dad doesn't know much about newer cars so he's wonder if its has to do with the way he put back the engine or that my mum might need another computer.