John,
I am not sure what directions you are referring to. Be aware that you can demagnetize neodymium rare earth magnets (if that is what you have) if you heat them to too high a temperature.
If these were the motor instructions, then I assume they gave you the correct temperature (heat the oven up, then turn off because every time the oven turns on to bring the temperature back up, you can get heat spikes from the radiation of the coils --if electric).
When I glued in my magnets using JB weld, I put the can with just glued magnets in my drill press, and then used a heat gun to warm the outside of the can as I spun it. This was more to allow the JB Weld to flow a little than to cure it. Also I kept my hand nearby to sense how hot I was getting the can. I could easily touch the can after I turned off the drill press. My particular Neodymiun magnets claim they can be heated up to over 200C, but I am still not willing to test that. Most Neodymium magnets are lower in their temperature ratings.