Wow thanks for all the effort grimm dingo. Unfortunately I had almost lost all inspiration for this. Maybe, though, you're edit will inspire me to really fix it up.

 I dunno why I spent over an hour doing this, but I did.

i.imgur.com/tp5dn.png

your's is really difficult to read, so I decided to pixel it from scratch from the reference image to see how I'd approach it.

1)  make sure the canvas is big enough to render out the details, and try to ensure they read at 1x

2) choose an appropriate palette with decent contrast 

3)don't be afraid to deviate from the source image to reinforce the clarity of the overall image

hopefully you find this useful in some way, making it worthwhile having done it  

I think its not about resizing the image but rather using more defined pixel clusters.

 Ok, thank you toxotes, I'll make it bigger.

 Try to simplify your pixels into bigger, more generalized clusters. Also, that black is what's giving you the most trouble -- using black to shade with is a big no-no most of the time because it's too strong and clutters the image. If you have to keep the black (which I believe you do), increase your resolution at least two to three times larger.

 Its not a down scale, but I'll try to clean it up a bit more. How might I make it more understandible?

This is quite unintelligible. Just looks like a down-scale of the original.