There are some big ones, but I don't see anything too large. It usually will give an error on the submission page if it has an issue. Your cart images will need to be converted to png, even simple free programs like mspaint will do this. As you said the images need transparency on the corners. This can easily be done with Photoshop or GIMP, GIMP is free so that is often a good starting point.
Here is the procedure for creating transparency. Once you have converted them to png files, open the png file in GIMP, click the fuzzy select tool, use it to select the section in the corners and click delete. If it shows a checkboard pattern on the section you just selected and deleted then you have transparency on that corner, if it shows white then go to Layer\Transparency and choose Add Alpha Channel and click the section again and delete so you see the "transparent" checkerboard. Do this for all sections, you can also use the Rectangle Select Tool and the Free Select Tool to select sections to change to transparent.
Once you have the image as you want it, choose File, Export as and choose where you want to export to. Et voila, you have an uploadable cart front image.
-There really isn't any place for the inside of the box scans. Please don't upload them as Fanart Background, this is the image shown on the background of your monitor when you click on the game. It should be a modern monitor size image related to the game, this is a background not a place for media scans.
Hope this helps.