So I've got them through now. This quick note is for the next person seeking help.
How it came together was something like this:
Download the tools from Mellanox.
There are two you can use; the MFT suite or MLXup, get them from here:
mlxup - Mellanox Update and Query Utility
All of the firmware downloads are found here:
Firmware Downloads
We need to get some info from the network card. Use anything you like to query the cards, be it mlxup.exe, mlxfwmanager.exe
Simply running mlxup.exe without any other syntax will query all cards. You will get an output like this:
.\mlxup.exe
Querying Mellanox devices firmware ...
Device #1:
----------
Device Type: ConnectX3Pro
Part Number: MCX312C-XCC_Ax
Description: ConnectX-3 Pro EN NIC; 10GbE; dual-port SFP+; PCIe3.0 x8 8GT/s; RoHS R6; hardware revision C
PSID: MT_2340111023
PCI Device Name: mt4103_pci_cr0
Port1 MAC: 980xx9xxxxx
Port2 MAC: 980xxxxxx
Versions: Current Available
FW 2.42.5000 2.42.5000
PXE 3.4.0752 3.4.0752
Status: Up to date
The hardware name is what we can use. PCI Device Name: mt4103_pci_cr0
Now if we were out of date after running mlxup.exe it would ask us if we wanted to update. If we said yes, it will automatically download the file from Mellanox and install it.
Now if we wanted to use our firmware or a different firmware that mlxup.exe wasn't aware of, all that we need to do is add the device and image file we wanted to flash with the -d and -i switches.
Our command would now look something like this.
.\mlxup.exe -d mt4103_pci_cr0 -u -i my-image-file.bin
The (-d device) comes before the (-u update) and then the image file we want to use (-i image-file).
If you are trying to flash a Dell card (like mine) back the standard Mellanox firmware, for example, you will need to add some more parameters to the command to make it flash your image file.
I have found that switching to the program called flint (which is found in MFT Suite of tools) and adding the following to the end of the command will allow it to run the flashing process.
-allow_psid_change burn
Now our whole command looks like this:
.\flint -d mt4103_pci_cr0 -i my-image-file.bin -allow_psid_change burn
once you run the above command you will get something like this:
You are about to replace current PSID on flash - "EMC0000000002" with a different PSID - "MT_2340111023".
Note: It is highly recommended not to change the PSID.
Do you want to continue ? (y/n) [n] : y
You must answer yes to get the flash through!
The flash won't take long. When it is finished do a full shutdown. Then boot up in the normal way.
All done.
Hope that helps.