Hi ,
-The example that you want to flash it will depend to the example that you want run.
Please take a look for the documentation, Kinetis Thread Stack Demo Applications User’s Guide.
8 Demo Functionality Overview
C:\NXP\MKW41Z_ConnSw_1.0.2\docs\wireless\Thread
-You can take a look for the next table in the Reference manual.
2.2 Signal Multiplexing and Pin Assignments

http://www.nxp.com/assets/documents/data/en/reference-manuals/MKW41Z512RM.pdf?&fsrch=1&sr=1&pageNum=...
-That lines are required if you are using Hardware control.
-Also you can find Low power Uarts Drivers
C:\NXP\MKW41Z_ConnSw_1.0.2\boards\frdmkw41z\driver_examples\lpuart
Hope it helps,
Mario