PIC32 acting as USB CDC HOST to FTDI
You don't need to use USB at all.  The interface to scanner is actually UART TTL levels.  SparkFun's demo is using an FTDI cable because they needed to hook up to a PC. You can just cross connect the TX/RX pins of one of the UARTs on your PIC32 with the TX/RX leads of the scanner.

Since you don't have any UARTs available, you can replace any of the existing hardware UARTs with a software bit-banged solution using two spare pins. That would seem to be easier than dealing with all the USB stuff.

Edit to reflect comments:

Here is code for a software UART in C. It is for the PIC16, but you should be able to modify it for the PIC32.  The code is interrupt driven, so assuming you don't have any interrupt pins (INTx) left, you can use any pin that is marked as an Input Change Notification (CNxx) which will generate a interrupt when the pin changes state.