The engine won't come apart, just keep going until you actually hit the rev limiter. It's somewhere around 5,500rpm or so when the case learn is active. Otherwise the normal rev limiter should be about 4,000rpm if memory serves me right.
I just gradually rev it up to cut-off and let it fall to idle. Though I did this through my aeroforce scangauge because HPT didn't always work with the older 2.24 software back 4-5 years ago. Never tried it with the current 3.6 build.
The readiness monitors should not matter, those will all take several drive cycles to either pass or fail depending on what they are.