It sounds like you've reached a good compromise there, between the heart saying you want to be canon-compliant as much as possible, and the head saying this is what is realistically possible to include. Sometimes the head gets it spot-on.

I've got too many specific details in there that we now know aren't what JKR imagined for them.

Isn't the key word 'imagined' in there? What you've imagined counts as well, and as an avid reader of Kaleidoscope I want to read what you've imagined for them within the framework of her story. Besides, it sounds as if - with the inclusion of the parts about his childhood and parents etc - you've got some of the best parts of the bio to refer to, and the freedom to continue with your own imaginings. Instead of finding it restricting, I hope the decision enables you to find it inspiring.