Would my dual snorkel scoop be affecting my cooling at highway speed?

Is your scoop connected to a sealed air cleaner (like the 6 Pack hood)? I'm guessing it's not, or you wouldn't be asking. I really don't think the opening in the scoop is large enough to create enough positive pressure to offset the much larger radiator opening. Plus, the hood is a low pressure zone, unlike the grill. With a shrouded fan, high temperatures at low engine RPM and high speed might indicate an inefficient water pump. But since you know you have dodgy timing I would concentrate on that. Determine TDC with a piston stop and mark the balancer. Then set timing to spec and reconnect the vacuum advance, and see how that goes.

I'm thinking right now that when you set timing using vacuum, you are not optimized for highway conditions. Without the advance, it might be too retarded at that engine speed. Both too advanced and too retarded can cause high temps, for different reasons related to inefficient combustion. So without some idea of where your timing is, it's hard to diagnose.