To me, it looks like the 2F is angled towards the rear pinion, and the split-case add-on e-brake is excessively low on clearance. I'm no expert, but from what I gather, it is hard to fit a 2F and 5-speed in a 40. The rear driveshaft looks really short. But that is all from the photos. The original frame middle crossmember has been removed. You might not have the motor mounts on the sides of the bellhousing.
Still, this is a nice 40.
I'd look into the details of the Weber carb, evidence of leaks, etc. I'd check for a VIN # on the frame. See if it is the weatherstrip or door fitment that is causing that or whatever. Details. On the radiator, or coolant reservoir, overflow tube dangling on the side of the frame rail.