Are you doing load development, or sighting in?
If I am doing my final sight in, I start with a fowled bore and shoot a 5 shot group, but I let the gun get COLD between shots......I want to know my cold bore zero (I always do this when the temps are as close as possible to the ones you will hunt in). Mostly for the ammo's sake...your cartridge warms up in a hell of a hurry when sitting in a warm/hot chamber and velocitys can clime with the temps). I do not worry about stress-induced shifting of groups....a bbl that has not been properly stress-relieved may start to walk shots when it warms up, and I should already know about it (see below).
Now, knowing the above, I always shoot a couple of long strings with every new tube. Heat it up pretty good. Start with a cold/fowled bore and just start shooting a big group( # of shots, not group size
) . If there is stress, it will show up. You only need to do this once per bbl (I feel). Also, it is almost a moot point with a custom bbl. BUT.....factory bbls may walk shots.
When doing load development, I usualy shoot 3 shot groups (hunting guns). I do wait for the gun to cool some between groups, but , unless it is very hot out, or you are shooting a whole bunch of groups, I don't wait to long. I never wait for a COLD gun....that takes all day!!!