Gaining confidence in your writing skills is a tricky task! I know I spent a lot of time before I reached a level of confidence where I felt comfortable saying "Yeah, I know how to write a story!".
My advice would be to practise. Instead of going full steam ahead and writing a big comic spanning multiple chapters and running over several years of updates, might I suggest doing something smaller first? A oneshot comic, perhaps, or less than 30 pages?
That way, you can practise the stuff you feel you're weak at - the plotholes and the twists seem to be the main thing - without investing all your time in it for years to come.
And in the meantime, you can tinker with the bigger story you want to tell. If it's plotholes/twists you're worried about, it seems as though the majority of your time needs to be spent tinkering with the outline and the planning. My advice is to worry less about how obvious your plottwists are, and more about filling in those holes - the obviousness of the twists don't matter as much, as long as there are no gaping holes in your story-logic.
Considering that it's your confidence that's lacking, though, I'm pretty sure those plotholes aren't as bad as you imagine. If you feel the need for a pair of more objective eyes, might I suggest finding someone to help you beta-read it before you release it to the wider public? A second pair of eyes can help judge your story's flaws better than you can yourself; we're nearly always our own worst critics.