Safely connecting signal GPIOs
You can and probably want to put these 1k resistors in series with your GPIO lines. Remember that if you need blazing speeds series resistors can be a problem because it creates a low pass filter together with the input capacitance of the pins.

About your second question, you can't put the base of a PNP in parallel with anything because you need two terminals to speak of parallel. This site and the whole internet is full of examples on how to turn on a led with a transistor so please try to search a bit and ask another question if you have problems. Nothing more than a base resistor should be needed, you will also need a resistor for the LED obviously.

You probably do not need a BJT at all though, and I don't see any additional safety that comes from it.