Without knowing more of the specifics I can recommend some general tips. It sounds like, from “knit everything together”, you have a bag of scenes that you started because you liked them but didn’t necessarily have how they fit together in mind. That’s ok but it’s a little bit the “we’ll fix it in post” approach - but that’s what editing is for! Just takes longer.

Ok, if that’s the premise I would say my favorite way to tie scenes together is by them ‘rhyming’, Fifth Element does this beautifully. Every transition somehow rhymes with the how the scene before it ended. It’s not a copy however, a character lighting a cigarette at the end of a scene isn’t matched by another lit cigarette but it could be a plume of exhaust from a car, or characters around a fire, or perhaps someone coughing from a punch in the stomach. All you’re doing is rhyming with how the scene before ended. Bonus points if it emphasizes the scene somehow, totally fine if it’s just a transition into something engaging.