i would check/replace the cap and rotor and the pickup coil (cam pos. sen.) that sits underneath the rotor in the dist cap. these 5.9's are notorious for that. also check the wiring to the ignition coil. have had problems with all of my magnum engines wiring getting frayed right there at the ignition coil.

 

I ran my battery low once and could crank the truck over but it wouldn't start unless I feathered the throttle. Once it started I could't taker my foot off the gas until the truck had been running for a while. I asked a mechanic at the dealer if the TPS needed to adjust itself he told me it did. New battery and no problem. I know you say it seems like its flooding out but I wonder if feathering the gas helps.

 

yes it does work on my '04 i've done it twice and it worked just as it should

 

he said he thinks but in order for fuel injection to flood the engine there would have to be so many simotaniouse problems it would blow his mind.