One of the reasons altering the valve clearance can affect engines and cause rough running is if you alter the clearance you alter the timing, it's the same with contact breakers on points systems. If the clearance is too tight the valve (or CB Points) open sooner and close late, if the gap is too wide they open later and close earlier.....it's all to do with when the cam lobe ramp has an effect rather than a running clearance. The other and more significant one is as mentioned in extreme cases the valve is open when it should be closed and some of the gases are getting where they should not be. Valves have an 'overlap' where both are open, the outgoing exhaust gases actually help draw in the incoming charge, if the gap is too close this overlap is affected and too much of the incoming charge goes straight out of the exhaust. If you have a decent exhaust gas analyser run the car, warm, at correct clearances and measure the HC and CO and then close the gaps just 0.002" and see what happens to the exhaust gases!
