What very keen eyes you have got!
1. The Clipper has two pitot probes on the left side whereas the other has only one and its placed further forward.
Yes, this is the same arrangement as the 737 Classics.
2. There is a small hatch under the cockpit window on the right side of the civilian NGs but on the Clipper that small hatch/panel is on both sides under the cockpit.
This is the cover of an external handle to open the Capts DV window from the outside. It was a standard fit to have this on both sides for the 737-200C but I have not noticed it on the Classic or NG before.
3. I believe it's the AoA vane that is under the pitot probe on the left side of the civilian NG but on the Clipper it is between the two pitot probes.
It is the same arrangement as the Classics. Why, I don't know!
S&L