I did almost the same on mine : I soldered the cables of the IR Board to a 2mm pitch USB header adapter I previously purchased not internet.
As I switched my case a fanless one (Stream NC2), I didn't need to drill a second hole : I just had to place the new IR Receiver close to the built-in one, and it worked !
About BCM94360, I switched my wifi card to a genuine Apple BCM94360CDAX with a mini-PCIe adapter. This card has 4 antennas (only 2 has to be plugged-in) and requires a full length mini-PCIe Slot.
The main advantage of this card in that BT Mouse & Keyboard are recognized in BIOS and Clover ...