A little update, there was a diode to the right of left alt which was soldered the wrong way around, i turned it around and now left alt works. Spacebar is still not functional.
Doesn't sound like a cold joint to me, that would take out a whole row or column just like a break. The controller looks to be factory soldered so I would rule out everything else before touching that.
I'm still waiting to have the pleasure of using Jigon but the jumbled keys behavior is what I'd expect if you aren't using the right matrix with matching physical layout in your mapping tool - do you get to chose or does it auto-detect what board you have? Can you override?
I don't think your problem is physical anymore, if you get the jumbled keys to work as expected and still don't have left alt it will be worth looking again but until then I suggest you put the soldering iron down 
The jumbled keys could actually be a weird mapping, actually the home,end,pgup etc cluster is totally weird in the jigon software:

So it's well possible, probable that the jumbled keys are because of a weird mapping, but it's weird since I thought this cluster was the same worldwide. But the thing is, I can't fiddle around with it and try to change it, since like I said before the mappings suddenly stopped working for me. I assembled the whole board and ran the Jigon software and was able to have some fun with it and change some keys, then out of the blue (I didn't do anything to the pcb, the board was assembled) the keymapppings reverted to default and I can't change it back.
I use the "connect" button in the software and then I change the keys and then I press update all like so:

however the changes are not applied to the board, when I press connect again I see the mappings revert to default in the gui in the software. The software doesn't ask me what keyboard I have I just assumed it realised that by itself.
http://kbdlab.co.kr/index.php?document_srl=2702787&mid=board_swHere is the link to the Jigon software. I used the loadfw.bat file in the L3FW_160422.zip to reflash. (L3 Trade shows All-xxx PCBs) file (which should be correct since the pcb name is reverse l3). I hope I'm not doing something wrong.
Were the smd presoldered? Otherwise it could be a diode soldered incorrectly
smd probably presoldered, lifez did the diodes. Are you then talking about a diode soldered the wrong way around or diode with a cold joint?
I also say check jigon again. Try and flash a default layout then try changing it again.
I had some weird issues where it wouldn't let me swap ctrl and caps lock until I flashed it a couple times.
Well, now when I try to flash it I get this error:
TLDR; The remaining problems with the pcb: Spacebar doesn't work, Some keys jumbled, possibly mapping related but the Jigon mapping doesn't work.