It is hard to see what has been done in the photo with the shears. Based on the other photos, I would...
- Fix the wood that has been cut off a few inches up. You could either replace the whole piece or scarf in a section.
- Before the wood, I would make a dam at the bottom out of - guess what? - Bondo.I would make it the same depth and width as the new wood will be; I would slope it from the inside outward: a ramp.
- On the bottom of the new wood I would also make a slope so that of the wood and Bondo are parallel. I would make the new wood about 1/4" shorter so that its ramp hangs over the one of Bondo. I would build the Bondo ramp up about 1/2-1: higher than the aluminum threshold.
- I would apply copper napthanate to the entirety of the new wood (you can get it at HD, it is used for painting cut ends of PT lumber). When the copper napthanate is dry - it takes a while - I would prime and paint the new wood with oil paint, then install.
- Finally, I would caulk the gap between the two ramps.