Motion: Drawing a Line from an Origin to a Destination in Processing

You've got a couple questions here, but I'll try to go through them one at a time.

Written as is, the lines draw very nicely, however my map of the US will not draw and I get an error stating The sketch has been automatically resized to fit the screen resolution.

My best guess is that Processing can't create windows that are bigger than the resolution of the screen. You can create a full-screen application, but really it shouldn't matter: you shouldn't tie yourself to one screen size; you should write your code so any window size will work. More on that later.

Anyway, to get rid of your first error, let's just use a smaller size:

size(810, 540, P2D);

But now you only see some of your lines, since you're always drawing to the same coordinates regardless of the window's size. Let's change that.

Notice these lines at the end of your draw() function:

stroke(64);
vertex(start.x,start.y);
stroke(160);
vertex(inbetween.x,inbetween.y);

Notice that you're using the x and y values of the vertex directly. This will only work as long as your window and vertex values are using the same scale. Instead, you should scale your vertex values so that they take into account the width and height of the window. One way to do that is this:

stroke(64);
vertex(width/1620.0 * start.x, height/1080.0 * start.y);
stroke(160);
vertex(width/1620.0 * inbetween.x, height/1080.0 * inbetween.y);

Cool, now we've got your lines drawing in a more reasonable scale. Next problem:

however my map of the US will not draw

Notice where you're drawing your map. You're only drawing it once, in your setup() function. But then you just draw over it in the draw() function with the background() call, so you never see it!

Since you're drawing the map and lakes as you load the file, doing that from the draw() function will slow your sketch down. Instead of moving any of your logic around, you could just draw your map and lakes to a PGraphics in setup(), then just draw that PGraphics in your draw() function.

To do that, you first have to declare a PGraphics variable at the top of your sketch:

PGraphics mapGraphics;

Then you'd change your drawing code to use that PGraphics instead:

  // Draw US Map
  String[] lines = loadStrings("Map2.csv");    // File containing coordinates to plot US Map

  mapGraphics = createGraphics(width, height);
  mapGraphics.beginDraw();
  mapGraphics.stroke(55);
  mapGraphics.strokeWeight(1);
  mapGraphics.smooth();

  String[] pieces = split(lines[0], ',');

  for ( int i = 0; i < lines.length; i++) {
    mapGraphics.fill(0);
    mapGraphics.beginShape();
    current = int(pieces[0]);

    while ( current == int(pieces[0]) & i < lines.length) {

      x = int(pieces[2]);
      y = int(pieces[1]);
      mapGraphics.vertex(width/1620.0 * x, height/1080.0 * y);
      i++;

      if ( i < lines.length) {
        pieces = split(lines[i], ',');
      }
    }
    mapGraphics.endShape();
  }

  // Add Lakes to Map
  String[] lines2 = loadStrings("water.csv");    // File containing coordinates to plot great lakes
  mapGraphics.smooth();
  mapGraphics.fill(22, 25, 180);

  String[] pieces2 = split(lines2[0], ',');
  for (int i = 0; i < lines2.length; i++)
  {
    mapGraphics.fill(110);
    mapGraphics.beginShape();
    current =  int(pieces2[0]);

    while (current == int(pieces2[0]) & i < lines2.length) {

      x = int(pieces2[2]);
      y = int(pieces2[1]);
      mapGraphics.vertex(width/1620.0 * x, height/1080.0 * y);
      i++;
      if (i < lines2.length) {
        pieces2 = split(lines2[i], ',');
      }
    }
    mapGraphics.endShape();
  }
  mapGraphics.endDraw();

Notice that I've also added the logic for scaling the map- otherwise, your map would be too big for the window!

Then you just need to draw that PImage from your draw() function:

void draw() {
  //hacky fade effect, change the alpha/transparency value to experiment with fade amount 
  background(55);
  image(mapGraphics, 0, 0);
  //...