Well done all fine. I would use wireframe x-ray view when trying to box select all those verts to delete or merge. That might be why you had to do a few separately, they may not have got selected first go.
And as FedPete says get rid of that now internal face that was the top of the cylinder. Can’t recall if it is done in the lecture but you do not want it there.
In wireframe x-ray mode, if you select the mouse selection tool ‘Face’, you can select any face in or out side the mesh. Experiment, Blender is very smart in this. Click front face selected, click again face behind the first one selected.
You got there but as FedPete says you can just ‘go in’ directly in wireframe. Face mode puts a dot at the centre of each face which aids specific face selection.