actually, timed "straight up" does not mean it is timed. Unless you check it, you do not know what you have. If it is an aftermarket cam, as you say, then you are trusting that the guy who first put it in knew what they were doing. Putting it in "per the timing marks" means nothing.
If it is a reground to stock specs cam, use the stock clearance numbers. Why do you need clearance?-as the engine heats up, the clearances close up because of thermal expansion of the valves-they get longer. the exhaust gets hotter than the intake so it usually has more clearance setting.
Rob