I drilled mine with the motor off, but I stuck the shop vac with the hose on the discharge side in the tailpipe. Just shove a rag around it and it will stay in the pipe. The only place for air to go is OUT the hole you are drilling. There's no way to get chips inside. 10 minute job and you're done.
What about the exhaust valves that are open?! You don't want chips being blown into your cylinder!
--Eric