Any dyno pull is tough on an engine.... But so is making countless passes on the road trying to get it to work correctly!!! If you are with a good dyno man, the whole process shouldn't be more then 2 or 3 pulls. The tune up process IMO is sooooo much easier on a dyno, be it chassis or engine, because all the specifics of the pull are right there on the computer print out...
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As far as being tough on a new engine, if it's built correctly and clearanced properly, no big deal....