Can the code in conjunction with the wiring have a destructive effect on the arduino? Or is it just a specific wiring mishap that may have caused some damage? It just seemed unlikely to me considering I'm only using 5V, ...
To me this is the most concerning statement as it indicates a lack of understanding of a basic concern/issue.
Yes 5v is plenty of voltage to cause damage. As others have said, over-current is what really causes the damage and with nothing to limit the current (like an in line resistor) too much current can easily flow and damage the AVR.
This is why directly connecting a pin to a voltage, +5, GND, or the output of a another pin that is driving a signal has the potential to cause damage, if the pin is ever driven.
The damage occurs whenever the pin that "should" be an input is changed to be an output.
sbrown:
I see, would the input on the pins still register as "HIGH" with said resistor in place?
yes
I've set all those PWM pins to inputs and the arduino won't light the green LED unless they read HIGH.
Calling them "PWM pins" is confusing people as PWM refers to a pin that is outputting a PWM signal.
You do not appear to be using them for PWM, so while the Arduino pins you may be using may support PWM, I would not call them PWM pins unless you are really using them for PWM output. Just call them "Arduino pins".
The Arduino pins you are using will always read high if you have things hooked up the way they are shown in the images in post #33.
In those images, pins 7,8,9, & 10 are all directly connected to 5v.
In post #12 it isn't clear how you have things wired up.
Overall, I'm still very confused as to how you have things wired up and it sounds like you have also wired things up a a few different ways.
A few things to keep in mind:
The AVR will power up with all pins as inputs.
The bootloader will attempt to blink the LED as it comes up after a reset, (but not directly from a power up).
The led on an UNO is wired up to pin 13. So if you have pin 13 connected to something that has voltage on it or is grounded, the bootloader trying to blink the LED will damage the AVR as soon as the AVR is reset - which happens whenever the reset button is pressed, or whenever you upload something.
--- bill