Hi @trunie1,
IClock, Pins and UART configuration is done via UI using S32 Configuration Tools. It is quite intuitive and has help (F1) information.
Clock (most likely it is already configured for you):

Pins:

Peripherals:

Here you will need to add/update the following 3 MCAL components: Uart, Port (for SIUL config) and Platform (for UART interrupt). You can use Uart_Example_S32K344 example project as reference:

You can find more information about Configuration Tools in "C:\NXP\S32DS.3.5\Release_Notes\S32_Configuration_Tools_Release_Notes.pdf". For further assistance on configuration please refer to S32 Design Studio community space.
1. FreeMASTER throws that error due to missing symbolic information. This information is extracted from the DWARF section of your ELF file. Refer to "Symbol files" (ch. 5.2 of the User Manual).

IF you already provided it, you can check the list of all extracted symbols by pressing the "View" button to double check whether that symbol was extracted.
Note: the ELF file should be build with enabled debug information.
2. Those errors are caused by helper functions/macros are not defined in your project. They are defined inside FreeMASTER project (not part of RTD/SDK). Even if you copy-paste the header file where those are defined into your project, it won't work because of different register notation (you saw it in case of UART base address).