Good news is that is a single sided board which simplifies matters somewhat.
Bad news is some of the cracks fall in very awkward places. You might think the two thin traces between A and B are not fun and you would be right but I would rather do 50 of those than one of those ones under the black stuff that makes up the contact pad of the switch.
Also I am not sure why more buttons are not working -- several of those look like they should trouble the C buttons and possibly even the start button. There might still be just enough connection though and they could go at any time so do fix them at the same time as the rest of this.
Step 1 is you need to stabilise the board, especially as this board will experience stress when you are pressing buttons and if it still flexes/moves that can make for unreliable buttons which is not fun at all. I don't know how much space there is on the back of the board for this. I would normally see this sort of thing in a power supply, retro keyboard or something big and bulky. That way I can stick a big thick flat sheet of something stiff on the back (another bit of PCB makes a good start) and then start on fixing things. Here though it looks like there was something that pressed under the right hand 0 and that tends to mean a lack of space to do that in. Unless someone dropped a screw or something when reassembling it and it got trapped resulting in that. You could cut down the housing to match the new thickness (looking at step 2 of
http://www.instructables.com/id/How-to-Disassemblereassemble-a-Nintendo-64-Control/ you might not even have to do that), however if you ever do want to replace the PCB with another one it makes life a bit harder as you will have to account for that (just stick another section of something as thick in there, however that is more than replacing the guts of the thing which is screwdriver + whatever you have to do for the analogue stick).
So assuming you stabilised the board I count 6 traces that will definitely need to be repaired and that mess around A could possibly do with a bit more work to be reliable but more on that later.
Picture
Red circles are locations of things needing fixing, blue highlighted section is the ground plane (if you look it comes off the negative of the capacitor at the top of the image, and also matches what you expect on the back side of the image) which does with the switching if you need another point to use. The one running around the outside is positive (it comes off the positive side of the capacitor) so try not to short it out. Just to be painfully obvious the one red circle leading to CD and CR has two traces under it so don't solder all together and treat them as individuals, if you do then pressing one of those will activate both buttons at the same time.
That one next to CL could be no fun at all as there is not much track before the carbon film part. If push comes to shove then you could go from the trace (or possibly that nice test point, the gold pad a bit further back) and snake a wire around the button part to go beyond the first button pad and somewhere in where the CL screen print is.
Everything else standard surface mount soldering fix -- scrape the solder mask off (go towards the crack lest you start lifting traces and that makes things far far harder), bridge with either wire or solder. If it is likely to go back somewhere that conducts (not likely here as it is just a rubber pad above it) then coat it with something which does not. Not liking one of the cracks being on angle but that is nothing major.
Don't worry about that little offshoot that looks like it should be coloured blue -- removing copper is expensive (and they were presumably making millions of these things) so you don't do it where you don't have to.
That mess around A... Everything contains two separate switches so if only one works it should still work. Also it is a carbon film thing so if you have stabilised the back properly then it will hopefully line back up and start conducting (it is a fairly thick layer of carbon compared to the crazy thin copper layers on top of a PCB).
I would not worry about that little cracked off corner from the other side of A.
Good luck and welcome to the world of electronics fixing. You have a nice little starter project here.