You're right, I'm studying the pinouts a bit more and it looks like REFCLK and WAKE are the ones that cause the trouble. SMBus is easy to split and JTAG is optional... Back to researching..maybe I can find a cheap IC and start producing these.
Don't underestimate the bandwidth involved here, even though it's relatively low for mining compared to gaming. Up to 64Gbit
for a 16x slot according to PCIe 2.0 specs. In reality the GPUs can't throw a stone anywhere near that number, but it's something to be aware of when choosing your IC. I don't know much about how the bandwidth is split between lanes, perhaps it's possible to bypass the IC for these data channels and let the motherboard handle it.
I'd assume you'd have to re-broadcast the clock signals to the connected devices, I think you're going to run into some latency problems here that will either be a major roadblock, or contribute to a lot of invalid hashes at least.
Note that i'm not trying to be a pessimist, just thinking this isn't going to be an easy task.