I recommend getting a mod called RCS balancer (or something). I know you aren't doing anything with RCS but the mod also shows your CenterOfMass when your fuel tanks are empty, so you can see in what way the CoM of the craft will change as you run out of fuel. Next thing is that you probably want to redo your craft in such a way that the starting CoM and the ending CoM (ending= out of fuel) are as close together as possible. This will make sure your craft will fly pretty much the same no matter how much fuel is in it. This will eliminate the need of pumping fuel around, which is not easy to do when you are flying.. especially for the more complex crafts. Continuing.. try to put your Center of Lift just in front of your CoM, and try and keep it there as you run out of fuel.. Also I dont recommend all those wings you used, better to keep it simple and use less but larger wings. I recommend a redesign