1st... We all make mistakes. I have made quite a few on the snowblower engine swap, so don't sweet it.
2nd, it looks primarily cosmetic to me. IF I was in your shoes... Yes, being a perfectionist might make it hard to let it go... What I would do. Machine up a couple of plugs that would fit inside that would sit a bit proud. JB weld em in (I can't weld!!) then take some light cuts on the lathe to true them up. A fresh coat of paint... no one will know the difference!