modeling the primary structures

(In Face Select Mode) Delete the Bottom Face of the Cube and then Delete the top Face of the Cylinder.

If you then can't connect two Vertices of the Cube and Cylinder, you may have Added the Cylinder in Object Mode, so the Cylinder and Cube are two seperate Objects and can't be connected.

If so, go into Object Mode, make sure both the Cube and Cylinder are Selected and one of them is the Active Object and then CTRL+J to join them.

You can add screenshots or video screen grabs to see specifically what you are having trouble with. We can point out the errors so you can correct.

Have you made it through this ppatthevisionary or need help?

Start again, that's always a great initiative, it's faster than to untangle the mess you got yourself in, believe me, I know. You learn a lot more because now you can see in advance where the wrong turn is and you start to develop and gain the Neo modeler's vision, where you know the best approach when starting something because you have already made the mistakes.

Eh,

What you have (left piece) looks completely different from the Cube and Cylinder from the Tutorial (right pieces) at minute 16, before combining the two:

I agree with Omar, start over.