Actually, I'm going to point you to a different guide, the SD Card Reader guide; it only deals with the reader.
Nintendo Switch Micro SD Card Reader Replacement - iFixit Repair Guide
There's a note at the final step about reassembly that you'll be particularly interested in.
During reassembly, make sure the press connector underneath the foam pad is firmly connected to the motherboard. It may help to remove the foam pad before reinstalling the card reader.
When I was writing the midframe replacement guide, the only issue I ran into was with the SD card reader; I hadn't gotten it plugged in all the way and had to open it up again and redo it. Removing the foam pad was the key for me; I could then feel when the connector snapped in place and once I reglued the pad and closed it all up again, it was all good.
So yeah, take @jayeff's advice and open it up and check that connector; with any luck that's all it is and you'll be up and running again soon.
Good luck; let us know what you find.
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