The 1st connection (vent to stove) should absolutely have a good bead of high temp silicone/caulk (500° minimum). A pellet stove has a positive pressure exhaust. So any spot that does not have a good seal? Will leak and that leak is letting CO into your home.
Don't feel bad. My stacks look like I was knee walking drunk when I piled them up. The first ton gets stacked OK, then my give a darn shrinks the farther I go. The important thing is they are off the ground, they aren't falling over, and come spring, nobody but me will remember what they looked like. Welcome to FHC.
Well, here's the final stack. We got all of the pellets out of the garage (top picture in my other post) and down into the basement. I think it's a decent stack - certainly no longer borderline pellet abuse.