sorry about your mechanical accident. I've done this twice on bikes that I thought I'd kept perfectly adjusted, which is why I now run spoke protectors on all my bikes (even the nice road bikes). The miniscule weight and "dork-ness" is a small price to pay for minimizing chance of damage from an overshift.

As to your wheel, it may be that the rim itself was bent when you shifted into your spokes.
But I'm not clear on: was the rear wheel in true after you replaced the spokes and re-tensioned and trued the wheel? Did the horizontal lack-of-true just appear later?
This may simply be your new spokes "settling in" - I'd go back and true it and re-tension the spokes, and see if it stays. If not, you may have to decide whether to live with an imperfect rim that's well-tensioned, or a poorly-tensioned rim that is true, or replace the rim.