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The two match on electrical ratings and land pattern, so choose purely by which side the common-mode choke should land on: the WHDG88409G puts it toward the low-numbered pins, theWHDG88403Gtoward the high-numbered ones.
The deciding factor is the PHY-to-RJ45 arrangement on the board and the element order in the PHY reference design, not performance — insertion loss, return loss, cross talk, common-mode rejection and isolation match item for item.
One group per port, eleven pins on each side: 1–11 with 78–88, 12–22 with 67–77, 23–33 with 56–66, and 34–44 with 45–55.
Each group holds four 1CT:1CT units — the four channels of one Gigabit port. Orient the WHDG88409G with the low-numbered side toward the PHY and the high-numbered side toward the RJ45, and each port's differential pairs run their own path without crossing under the part.
Yes. Every port on the WHDG88409G has four channels: a Gigabit port uses all four, that is two pairsets, while a 100M port uses one pairset and leaves the rest unused.
The transformer does not distinguish speed — the rate is negotiated by the PHYs at each end — so mixing speeds across the four ports needs neither a different part number nor a different termination. Dedicated 10/100 parts are listed in the10/100 BASE-T range.