One of my friends had a KH-202 that he left in his basement during a flood, and it ended up cracking the body. It then sat in his closet for 5 or so years before he asked me if I wanted it to try and fix it up. A closer inspection of the guitar (minus any paint) showed me that the body crack is insignificant, but there are two cracks all the way through the headstock, as seen in this photo: (the highlighted cracks run all the way through the headstock and can be seen on the other side)

My question is, what would be the best way to go about fixing this? My friend told me it was having tuning problems after he got it out of the basement, and that it was because of the body crack, but I think the headstock is more likely the problem.(?)
Tuning problems might be because the neck had coz of the water?

Cracks going that way arent as structurally bad as a break in the wood grain the other way on.

If you cant prize the cracks apart and get some glue in there, I'd drill a few of small holes from the side then put a few counter-sunk screws through to keep the cracks stable, fill the holes from the side and just do a solid finish over it.
Do what jscustomguitars said, but I would say to drill out some small holes and fill in with a wooden dowel instead of the screw. Before you put the dowel in, fill the hole with a good wood glue. Then use a chisel or sander to cut and smooth off the dowel so its flush the headstock. I suppose the screw would work just as good to...just be careful so you dont crack the wood even more from overtightening or from not drilling the right size pilot hole, since the edge of the headstock is pretty thin, it will be easy to crack it with the screw.
+1 but make sure you drill out the start and stop of the cracks to keep them from spreading
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