It's not your fault black PCBs are camera shy! The LED linkage is worrying so I'll ignore it and hope it fixes itself once the switches work properly.
Looking at the new pics all the diodes are connected to the bottom/right pins and the diodes connect up the columns which hopefully means the top/left pins connect across the row, you're not missing alternate keys so hopefully it is the whole row. That means if you bridge the left pin of one of the switches on the left of the spacebar to the right pin on a 'dead' switch (or as they have no solder the pad around the pin) it should type the 'dead' key. Or with dots:

Bridge
blue (you probably need to go to the next switch over as space doesn't work but you get the idea) to
cyan and it should type Alt (I assume). I'm not entirely sure what's going on below the orange dot - could just be some loose solder on the surface or could be damage. I think all the
green traces should be connected so if blue->cyan doesn't work try blue->
magenta and that should type Alt. If blue->magenta works but blue->cyan doesn't solder a bridge between red and magenta, then blue->cyan should work. If it does solder between blue and
orange and the switch should work as normal.
The trace going down and left under the orange dot looks to go back to the controller chip so if there is damage there you could have a problem - if that connection is supposed to be grounding the keys on the other side that could explain their ... actually I'm still not sure if these keys are working (continuously pressed when held) or if they are click-unclick-click-unclick-ing. Try and clean up that area and check for damage, you might need to scrape the trace as I don't think you want to try soldering to the controller pin (a member sent their board off to a professional PCB repair place and they wouldn't even do it! Somehow he did it himself out of desperation so it's not impossible, but easier to scrape the trace as you can see it)