This looks wrong:

I’d slide those edges together and Merge them.
There is a weird angle here:

Try to avoid concave quads like this one (all ‘inner’ angles should be less than 180°, if possible):

and these Faces should probably be ‘flat’ (lie in one plane):

In this case you can simply use S, Y, 0.
Now, all these work together, so changing one, will affect the other problems, but if you tackle them in the given order, you should be good, I think (but check that!).