I should note I did the same thing you're doing when I upgraded to angel eyes, which have since been swapped out once or twice already. Buckets got cut, they're really only there to fully support the stock headlights, and if you're not using them...
Might be worthwhile to try and fabricate your own buckets and brackets. Don't know what the "mistake" you refer to is, did you not get two sets? I can't imagine it would look good at all with just one set of headlights swapped.
As long as no screw holes are touched, and everything is still solid enough to not bend, you're fine. There's a TON of metal that can come out without sacrificing anything really. (As for part value, I wouldn't bother worrying about it. It's not a commonly requested part, and there's enough parts cars out there to grab one from if you screw up too badly).