Hello!
The problem is with the functions you are selecting for each pin, you left everything with the Function 1 and this is wrong, since the functions change for each pin. You can refer the user manual of the LPC54618 (UM10912.pdf) in the chapter 10, table 256 you will find a table where you will see all the different functions for each pin.
For the SCK you are selecting port1_pin9 in function one. In the image below you can see that the correct function is the number 2 in order to be the SCK of the SPI1. 
For the MISO (port2_pin4), MOSI (port2_pin3) and SSEL (port2_pin5) you selected function one. However, for these pins the correct function is number 3, as shown below.

Your code should look like the following.
const uint32_t port1_pin9_config = (
IOCON_PIO_FUNC2 |
IOCON_PIO_MODE_PULLUP |
IOCON_PIO_INV_DI |
IOCON_PIO_DIGITAL_EN |
IOCON_PIO_INPFILT_OFF |
IOCON_PIO_SLEW_STANDARD |
IOCON_PIO_OPENDRAIN_DI);
IOCON_PinMuxSet(IOCON, 1U, 9U, port1_pin9_config);
const uint32_t port2_pin3_config = (
IOCON_PIO_FUNC3 |
IOCON_PIO_MODE_PULLUP |
IOCON_PIO_INV_DI |
IOCON_PIO_DIGITAL_EN |
IOCON_PIO_INPFILT_OFF |
IOCON_PIO_OPENDRAIN_DI);
IOCON_PinMuxSet(IOCON, 2U, 3U, port2_pin3_config);
Also keep in mind that the example is using the Flexcomm9 since it's using SPI9. You want to use the SPI1, so, you will need to use the Flexcomm1.
Hope it helps!
Victor.
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