Gotta blow air at the rad. Or at least spray water on it. The engine fan alone can't be making enough air flow to cool it down at higher temp. Engines run hot on break in as is already.
This thing has all the ingredients for getting hot on the breakin.
1. No fan blowing on it.
2. A flex fan
3. no shroud
4. Low timing
5. Minimal radiator
I'm not saying all the above should be done, but almost any single one of them done would probably solve the heat problem.
Also go ahead and drill that thermostat and put it back in.
Why have to concern yourself with air in the coolant ever, let alone on a stationary engine on a breakin.