The first thing you ever want to look at when there are questions about your outputs is the Overlap Report. In yours, you can see that there are a lot of reds and oranges and yellows. That's a bad thing. You want everything to be a blue. This means you need to use more overlap.
Also, in the areas you are concerned about (silos and stuff) they will get less overlap because they are taller and are closer up to the camera. You will need to either add extra images of these objects, flight higher, use more overlap or all of the above to get them to turn out properly. Your source imagery needs to have at least 10-15 looks at anything you want to turn out well.
The camera busy message means your SD card can't keep up with the write out speed and you might need to choose a slower one in the Map Pilot settings to keep from dropping images.
The arrows at the top of the Map Pilot screen are direction indicators for keeping your remote centered on the aircraft which is important for maintaining signal strength.
There are a lot of moving parts to aerial mapping. We try to handle as many as we can but there is a learning curve. This is pretty good work for one of your first maps though. Keep it up!