I'm not sure I'd reccomend a full rewrite, but perhaps at this point it'd be a good time to take a step back and refocus. I'd really suggest taking a brief hiatus and digging into your story further.
When you're working on a long form narrative comic, unlike gag driven comics, there's a lot more in depth plot development going on and if you're winging it, you're just going with your first idea and not giving yourself the time to edit and rework.
I definitely ran into that problem early on, but I was lucky enough to have the help of other talented writers around me. They pushed me to work out the story fully, not just by knowing the next page, but by knowing key points along the way. My training comes from a basis in screenwriting and the techniques used there talk about 'beating out your story.'
This basically means finding the big key points of your plot and boiling them down to the simplest sentences you possibly can. From there you branch out.
Here's a place where you can find out more about beat sheets and why they're SO awesome for helping plot out stories. They're a literal skeleton which you can build on top of.
-> http://storyfix.com/beat-sheet-basics-101-plus
And another place where you can explore and even download a worksheet to help you figure out the basic stuff -> http://jamigold.com/2012/02/how-to-revise-for-structure-part-two/
I REALLY suggest you taking the time to reverse engineer a story before you work on your own. It'll give you a better idea of how it's used. When I did this I reverse engineered Lilo and Stitch and it was a SUPER helpful exercise.
TL;DR - Google Screenwriting Beat Sheet (no it's not music, or porn) and learn you a thing about writing plots.