Hi, 

There are better ways then rmmod -f.

To reload a new firmware to PRU, you can just use /sys bindings.

Demonstrated here :
https://github.com/ZeekHuge/BeagleScope/blob/master/examples/firmware_exmples/pru_blinky/deploy.sh#L66

The same repository has some examples. And I am working on a few more. 
Further, there are some tutorials on https://zeekhuge.github.io and there 
will be more soon.

As for the pin configuration problem,
'Universal IO' owns all the pins of the board, so your the pins in your 
device tree file must be conflicting with the Universal IO. You may check 
this in your dmesg.
To configure a pin you can mostly use config-pin
I have described its use here in the 2nd point under 'startes'
https://zeekhuge.github.io/post/a_handfull_of_commands_and_scripts_to_get_started_with_beagleboneblack/#k_dev:01d25bfd2399ec47b9c04f156786eab8

Good Luck with PRUs. I will keep adding content and example to the above 
mentioned links as I move along with my project.

PS : you should probably disable the hdmi cape, if its not being used.

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