It seems like you've got a good understanding of most things. But i think one problem with the crane rope would be that the centre of the 4 connecting 'ropes' isn't centred. I'm not particularly good at isometric stuff, so i cant help you there, but it's worth pointing out. I think once they are centred, the lines won't be so jagged, and therefore easier to work on to make look smooth (using selout/AA).

You can also find the center point by dividing the top of the rectangle into 4 then draw a straight line up. Best if you have layer capabilities, but can be done with paint too. Just erase them once you find true center.

Thanks for the help guys. I'll inform you of how it goes...

There is no line configuration that will give you smooth lines using this size box. I tried and failed out of curiosity. Since the most jaggy area is over the top of the box. Texture the box in such a way when coloring that you minimize the jaggies. Use AA or if say you are making this a wood crate you won't even need to bother. On your new update the front right hand rope is using the worst possible iso line 221221221221221. Change that to 1111111111111 and widen the box to meet the edge if you can resize the box. If the box size is not critical but the smooth rope is then start again by drawing the ropes first and let them determine the size of the crate.
22122= 2 pixels then 2 pixels then 1 pixel and so on.