What's a good wait time between dyno pulls? My shop says about 5 min for engine to cool down, if it's still too hot then the results won't be accurate(lower HP)
Does it really have to cool between pulls?

 

I wouldn't think it would matter much.If you are going for the highest numbers possible cooling the engine would give somewhat higher numbers just from havibg a cooler intake charge.Consistent numbers,and a more useful/safe tune,will come from an engine at operating temperature.
I would run the dyno fan through the radiator and let the engine idle awhile after the run to cool the pistons and other internal parts to a normal temperature,then shut down.By the time you look at the results and decide what to change the engine should be ready for another pull.
I got a couple of freebies at a car show once and they were back to back,mere seconds between runs,and there was hardly any difference between the two.