You can easily run stock rods. It's the rod bolts that are the weakest link in a stock rod. Get F2 rod bolts for a bit of insurance. Mike Rieck can probably sell you a set.
As for break-in, if you check out my build thread, linked below, you'll see a video of one of three heat cycles and then a video of us breaking in the motor - on the dyno. If everything is fresh or new, bearings, rings, etc., the motor will be tight and run hot -- but that's the only concern with breaking it in this way.