How do I clip parts of my Inkscape diagram such that its corners are perfectly rectangular?

I've been trying to edit a SVG diagram (here in my Google Drive you can find it if having the original SVG helps you in assisting me), below is a PNG bitmap of the original labelling what I want changed.

1. 
   

   If you zoom in where these arrows are (and other places where the pink arc intersects with the dashed line) you will see that while I've lowered the pink arc so that whenever it intersects with the brown line (i.e., the dashed one) it is hidden under the brown line. The problem is that since it is dashed the pink arc is still being displayed whenever they intersect a gap. So what I would like to know is how I can overcome this problem. I'd also like to know how I can convert the gaps in the dashed brown line into a new set of dashes, but of a different colour to the colour of the original dashes (i.e., brown) so that there is no white space here any more.

   
   


2. 
   

   How do I make the sides of my drawing nice, homogenous (in shape, not colour) and rectangular so that there are no gaps or curves sticking out of the sides of it. The label 2 in the below bitmap shows some examples of what I mean, like where the brown dashed line extends past its intended bounds or where the brown cell bed below does not line up with the edges of the pink bucket-filled area.