Hello!
I have found some solutions than may interest you.
It is possible to combine the two given devices and make them work at the "same time" (I mean the 40 pin connector and the USB 3.0) by using a SATA Multiplexer/Demultiplexer IC, like this one:
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And an another SATA to USB3.0 converter IC like ASM1053 or ASM1153.
If you have any other requirements, ideas, or questions, let me know, please and we can discus.
About the time. Using the above, briefly described approach, I think the PCB could be routed within 10 days, even quicker.
P.S.
I think, your mSATA SSD (mini-PCIe) to USB-3 adaptor are also made by using the ASM1153, but not sure.