From the description my understanding is you are using CYUSB3KIT-001 (EZ-USB® FX3™ Development Kit (CYUSB3KIT-001) | Cypress Semiconductor )
What is the version of the KIT that you are using. This is available just next to J77 or below J96.
Your settings SW 25, J96, J97 and J98 settings looks fine.
What is the setting that have you used for SW9 (In buse power and external 5V DC)
I am not sure if you have to short J40 & J47.
Instead of external power when you bus power the device any of the LED's glow on the board such as (D14, D15, D16, D17 & D18)
Thank You & Regards,