I have to say I do not understand how you managed to get to such a bad place with this kit. I've done six of them and never used any filler other than a bit of CA glue along the cowling centerline. One thing that has to be done with all these modern kits is to clean off all sprue nubs COMPLETELY because the fit is so precise. One thing I have discovered (the hard way) with this and other modern kits is to take time to very carefully mate jointing surfaces; the slightest little imperfection on the mating surface will throw things off, and then it's like rolling a snowball downhill, the problems just expand and grow.
You've done a good "save" here, but I think the future solution is to be really precise with getting the parts off the sprue and cleaned up. It's a never-ending fight. I was just working this past week on an Eduard Spitfire and couldn't get the wing and fuselage joined (a notorious tight fit) and then when I looked closely I saw the tiniest bit of sprue nub on the inner edge of the upper wing. smoothed that and sanded down, and - bingo! - everything came together.