Rockford Fosgate Prime R300X4

Learning to draw is part of it if you want to make your life easier. Don't necessarily try to draw everything, just as much as you need. Many times, if you can find something close, like the AQ diagrams, you can just mark them in the PDF with the different circuit board designations/circuit paths and save them as a different file name.

Is the amp still in protect with the voltages above?

Your meter isn't as fast as your scope, is the pulsing on the scope, approximately what you'd expect from the meter readings?
 
It is still in protect. Its back to flashing red and blue. I now only have a resistor and diode unsoldered. Both coming off pin 3 of 358.

It is fluctuating on scope about as fast and meter is. Especially looking at graph on meter back and forth.
 
If you're going to markup an existing diagram, load it in something like PDF exchange editor and save it as whatever you'd like (don't mark it until you save it as a different named file).

In PDF EE, you can draw lines, add text, photos... Whatever you need to do.

I don't have a good program to use for diagrams but you want something where you can add whatever you want to add and it has a grid you can snap to to keep things neat. If you may think you'd like to simulate circuits, a circuit simulator may interest you. Something like TI's simulator may work for you. If someone else has a suggestion. feel free to post it.

If you can bear to use paint (yuk), paint.net (name of program) may interest you. It's FAR better than paint but still a bit strange to use.