This is what I do when breaking in a newly built motor and it has worked for me without fault.
1. Run engine for 25-30 minutes @ a constant 2000rpm. (Especially if running in a new cam.)
2. Immediatly change oil and filter while hot. (Gets rid of anything that may have gotten into engine durring build up and initial startup flakes of metal from cylinder walls and rings.)
3. Run conservativly for 500 miles. (No raceing or high revving, always staying below 3000rpm, making minor adjustments to carb settings, timing, etc. as needed.)
4. Change oil and filter. (I know it can be a PITA but always change oil and filter when engine is at normal operating temperature, never cold. But you already know that i'm sure.)
5. DRIVE IT LIKE YOU STOLE IT!!!!
I have built many engines over the last 25 years and with this process I have never had an engine fail. Mind, this is just my way. Others may have just as good of processes they use.
Cheers, Carl