Freakey, the stain seeping into cracked binding actually happens quite a lot. I have never seen anyone on the forum actually "fix" it or come up with a solution. Everyone I've seen just does what you are doing and changes their vision for the guitar to a relic build. Its actually a pretty cool effect which you cannot replicate. I bet Dedman is chomping at the bit.

Good luck mate I'm sure you'll get this build back on track.