First of all, congratulations on a difficult repair; that charging port replacement is something I'd definitely have second thoughts about attempting!
Going over the steps required to pull the motherboard, it appears you have to unplug both speakers as part of the process. My strong suspicion is that one or both of the flex cables connecting the speakers to the lighting flex may not be fully seated. With those ZIF connectors you can't always tell for sure the cable is fully seated. If it was mine, I would open it back up again and reseat the speaker connectors.
Unfortunately, both of those speaker cables are ultimately routed through the lightning flex, so if reseating the speaker cables doesn't help, the the next obvious source of problems would be the solder job on the motherboard. Ouch, hope that's not it, so check those speaker ZIF connectors first.
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