I sense your frustration, but this is a different story now 
I am – despite using OH v1 for almost a year (on and off) while building a house; I am still a novice. 
When I say architecture, Iuse my rPi for OH and MQTT and that’s it (self-contained, defined function).
The Arduinos is a platform I use to interface with whatever ‘thing’ I need to interface; windows, HVAC, lights, sensors, etc. These act as sensor aggregators, and protocol converts (if you will) from I2C, SPI to MQTT.
The Arduino is a micro-controller board with a bunch of analog, digital, and other inputs/outputs. programmed in C via the Arduino IDE (or sloeber).
Also meaning, I have not done any OH <-> rPi GPIO set-up or integration; I am sure you can look up the GPIO binding and maybe other chime in.
I agree in principle though, that the the ON|OFF items, like PIR and LED can be driven via GPIO (be mindful of power draw, and the tPis capability / specs in this space).
Your rules:
Rule "PIR"
When (pIR. State==ON)
then
Led. SendCommand(ON)
should rather look like this (watch spaces, upper / lower case, rule construction):
rule "PIR"
when
MotionSensor changed to ON
then
Led.sendCommand(ON)
end
Well, I wouldn’t dare to figure out OH in 3 days – I am still trying 
Also, are you using OH v1 or v2?