That's a pretty tall order given modern coolers are seldom available with S478 mounting hardware. The only reason Noctua coolers work is because their SecuFirm2 mounting system hasn't changed since then so old parts fit onto their new coolers.
I'll suggest the Noctua NH-L12 which is exactly the same height as the NH-L9 you mentioned (provided you bottom-mount the fan), but 120mm fan instead of 92mm. These are even shorter than vintage heatsinks that were available at the time like the Zalman CNPS8700. The CNPS8900 Extreme was another 5mm shorter though, at 60mm. But you'd have to check if you have room for a 120mm or 110mm fan around the socket.
I don't care for how the stock coolers bend the motherboard