Wow David... This is a tragic setback. How fortunate you didn't toss the "orca" against the wall. I'll bet you were tempted.
Step back and count to 3... Not one, nor two, but three !
"First shalt though take out the Holy pin. Then, shalt though count to three... No more. No less. Three shall be the number though shalt count, and the number of counting shall be three... 🙂
But you can prevail. I would recommend staining or even painting the wood you plan on using prior to gluing it in place the next time. Just a thought.
I have never seen anything like this before. I have encountered small areas of wood that would not take a stain coating properly after using cyano glue on them first. But never at this level.
Hang in there buddy... you can do it.