This is a very old post but surprisingly has yet to get a reply - is no-one using a LoraWan module with the fire (or with a GPS)?
The answer to the original question is that for some reason the designers of the Fire decided to use the only serial connections guaranteed to clash with pretty much everything - GPIO16/17 (a.k.a Serial2).
Both the GPS and the LoraWan module are wired up to use GPIO16/17 by default (again, designers - what were you thinking???) but both have links on the board to allow alternate pins to be used.
The GPS has PCB tracks linking the defaults which must be cut to allow the use of the alternatives - GPIO 3/1 or GPIO 13/5. (This is what the note is referring to I think.)
In the case of the LoraWan module the links are made with Zero ohm resistors and you can move them to link to GPIO5/2.
Unfortunately this is where you and I (and anyone stumbling across this old question) hit a brick wall because the documentation for the serial ports seems to be non-existent.
Hopefully someone else can shed some light on this.