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Hi .I don't think a 390 flywheel will work with a 460.The 400 has a 180 tooth ring gear.I think the 390 has a 184 tooth ring gear.Not sure if they are ballanced the same.
Ford was pretty cute about the starter issue, so if it bolts up, it'll work, basically. A 302/351w starter will only fit a 302/351w bellhousing, an FE starter will only fit an FE bellhousing, and a 385/335 starter will only fit a 385/335 series bellhousing.