it’s easier at times to not join things, particularly if the shapes are simple. I extruded everything from one cylinder with no caps and used a boole to cut the hole to extrude upward. The boole could be used as you did to create it all at once but even if it’s all set up to make a clean mesh you still get different results (sometimes odd) if the caps are turned on or not. As I said, easier to extrude as long as the shapes are fairly simple.
To make the mesh clean I reduced to two height segments for the horizontal cylinder (has to be two to make the boole cut clean, at least in this case) and only one for the vertical. The two cylinders need to have the same number of rotation segments so the edges all line up. Finally they are lined up so the bottom of the vertical cylinder is exactly at the center of the horizontal one.
I uploaded a new version with the partial build as a boole and the initial poly before extrude.
https://homepage.mac.com/bdjones/.public/L1900SDS.zip
If you don’t already, use the extrude shortcuts, particularly Shift while extruding to change the extrude angle on the fly.