I believe the red paint was used on all "critical" fasteners. I believe we've talked about how it was used on brake components and elsewhere in the car where the fastener involved a component that was crucial to the safe operation of the vehicle. In the case of the rear axle plug, if the plug were to come out, the rear end could ultimately lock up causing a serious control problem.
As to the orientation of the exhaust clamps, I checked the 1964 and 1970 (I don't have '65 thru '69) and all of them show the clamps with the nuts down. Interestingly on the 1964 V8 exhaust pipe, the right rear bolt at the manifold is installed with the bolt head down, while all others have it up. I believe there was some sort of clearance issue on the flange of the manifold. The '64 manual also showed a retaining clip on the right front bolt. If I had to guess, I would say there was likely a small machined flat area on the flange of the manifold and this clip would help to keep the head of the bolt from spinning as the nut was run up from underneath. As I said, I don't have a 1965 book so I don't know if this practice was carried over.
