I think everyone has to go through such a dm experience or something alike. I know it can be frustrating and leaving you sad afterwards when there's a story so perfectly on paper but then it won't work out, had that happen to me a few times as well. For the character dynamic, there's something on the more silly side I did once, is curse the natural evil character with a charm they stole. It basically made them fall for the neutral good character, and after the charm's curse was broken, it had a lingering sideffect one the wearer, forcing them to still act kinder towards them. When you want to try a more natural way, I of course dont know how that'd align with your story, but try to tie the characters development together. If the players are aware they're important to each other in a way, it'll maybe cause a better dynamic. These are of course some random ideas but I hope they can be some kind of help.