1. Before you do anything else, remove the 120r resistor from between CanH and CanL.  
   We're going to mount the module face down on the back of the proto board and then it'll be too late.
2. Have a look at the back of the module and see if the markings are opposite to what they should be.  If they are, just erase them with a felt tip pen;  maybe save yourself some head scratching later.

To transfer a circuit to a protoboard, I draw it in up in Inkscape and print it on a clear label and stick that on the component side of the board. If you want to try it, use the first image below. 

I've also uploaded the Inkscape file.  Even if you're not familiar with Inkscape, you can play around with the different layers, and copy and paste pads and traces.

In any case, you can use the second image as a guide.

Also, if you're going to drill the four mounting holes, this is the time to do it.

The horizontal lines are just for reference. They match the traces on the copper side.

Solder in the six jumper wires and trim the tails.  You can just use resistor leads for these.

Solder in the dual row right-angle headers from the top of the board.

Solder in the 6-pin straight header for the CAN module, long ends down. The header is shown in blue. Go easy on the solder here, and do not trim the tails. And do not solder in the CAN module.

On the top of the board, cut off the short ends of the pins flush with the plastic spacers, so the header will fit under edge of the blue pill:

At this point everything should look like this:

Drop in the pins for the processor board, as shown:

Fit the processor board on the pins:

Solder in the can module on the copper side of the board, so it looks like this:

If you test fit the CAN module, you'll see where you need to trim back a couple of the RA header solder tails. 

And that's it;  you're done.