Creating footprints in Altium is very easy, its just a matter of starting your own footprint library, creating a new entry and drawing the line/holes you need while using the measuring tool to check it matches the datasheet. (in your case the drawing pdf)
Then adding your new library to your project.
A search on youtube should find videos of people making footprints in alitum.
Altium makes it even easier because you can copy/paste any existing footprint into your new footprint library. So you just need to find something that's close and adjust it as needed.
Adding 3D to your models is pretty easy too, just place a 3D body and give it some dimensions.
However molex have 3D models already available, so you can just import those for the 3D part.