Hey Mala,
I made a couple brief videos with your model and geometry to give some insight as to what you are looking for.

Here is one that shows the main culprit. But I also use this to show you "rebuild" and also talk a little about a common error made in "adhering to some unrealistic tolerance"

The CAD modeling will model things to pretty tight tolerances. even at unrealistic levels. Think a microscope on a razor blade. At some type of zoom, the sharp blade will look like the edge of a rock!!!

So applying your understanding of what may be needed (A welder fills in gaps on pipes) you can adjust expectations to meet the real world and get great results!