It would be normal for the exhaust to come out only the left side until engine warms up and the heat riser valve in the right exhaust manifold opens up. Exhaust manifold leak shouldn't be causing idling problem.
What color is the smoke? White indicates excess water present, blue indicates oil present, black indicates incomplete combustion of fuel (running too rich).
Something else to check is the PCV valve. If it is clogged up or stuck open, it will affect the idle. Spring-loaded plunger inside valve should rattle when shaken by hand. Another check is to squeeze off the ventilator hose to the valve while idling. Engine speed should drop at least 60 RPM with hose blocked off.
Another item to look at is the vacuum advance unit on the distributor. Does the slide bar into the distributor move as engine speed increases? It ought to move as well when disconnecting the vacuum hose while idling. Hose is supposed to be disconnected temporarily when setting the timing.
Attached are are a couple of pages from the '65 Gran Sport shop manual supplement. The #1 plug wire goes in the hole just to the left of the window. Rotor position is shown for timing mark on balancer at 2.5 deg BTDC.
The supplement also notes the original carb is a Carter AFB model 3921S for automatic trans cars. The original transmission is a Super Turbine 300 2-speed code NK. The 400 engine is stamped on the block with code LR.
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