I believe the original 340 trays will not because they have "round" holes to secure them to the special main cap bolts. Later windage trays, Direct Connection or later OEM were made with elongated holes to fit the 340 main cap bolt spacing as well as the wider 360 main cap bolt spacing.
I don't recall ever hearing about 340, 360 or 5.9 Magnum bolt length being different. But perhaps someone may know for sure about the 5.9.