Wow I will try to help I do not have pictures yet of my car to show you.
However, the break lines should follow the axel tube as in being in contact with it all the way down the tube.
Someone may be able to post a pictures for you I will see If I have any..
The dana 60 aftermarket cover is larger than a stock one obviously did the manufactures say it would work with a stock tank? I would think if at full compression of the springs if you have about ½ inch of clearance you should be ok with it. You have some nice stuff.
Hope this helps.