So I need to reroute the USB input port (the original Micro USB port on board) to another USB female connector. Will I need to desolder the Micro USB port and use the pads or if I can just use pin D0 and D1? Will I need to use a level shifter/resister voltage divider? What kind of speeds are needed for the level shifter? Any recommendations?
How about the host port? I think I can directly connect them to 5v? The Teensy 4.0 breakout/evaluation board have the D+/D- directly connected to the pogo pins for the host pins.

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This is my USB C port, to replace the Micro USB port. It is in device mode (the pulldown resister to CC pins) so it can actually draw more current to charge the lipo. A6/B6 or A7/B7 goes to D0 or D1? The TX RX D+ D- thing is quite anoying and I am not sure which one is corect.
Also the host port as well, D+ to D+ and D- to D- on the SMD pad under the Teensy?
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It is not very clear on the T4 breakout/evaluation board, it looks like D+ is directly connected to D+ and vice versa. 5V logic level...

BTW the USBLC6-2SC6 ESD protection chip's I/O1 is connected together, and I/O2 as well. Not sure if needed.