how to remove extra material in solid part?
I removed all the extra stuff with my favorite trick for getting rid of unwanted junk on a model, the 'delete face' feature. Make sure the option 'delete and patch' is selected...
I used 3 features since to me there was 3 unique issues, but you could also pick them all at once and do it in 1 feature.
The first eliminates the unwanted exterior material, the second eliminates the little cuts in the 'thru' tubes, and the 3rd eliminates the undercut at the bottom of one of the internal geometries. (gate valve pocket?)