So just to put a happy ending on this story, I bottled 6 weeks ago and had my first bottle last night. It turned out amazingly well - not too dry, not too sweet - way beyond what I expected given all the drama this batch endured.
I've still got some of this older grain, and given how well this batch turned out, I have no second thoughts about using it all up now. My only question is what's the best method for introducing the amalyze enzyme which is clearly needed for older grain? Should I use it during the mash, or repeat what I did on this last batch and mix it in as it goes into the fermentation tank?