For what you want to do, w/ the engine in the engine bay, I would definitely use the Scotch Brite pads. I think any other type of abrasive wheel, such as the brass cleaning wheels you had mentioned will be too harsh on the head surface - plus you do not want to take off any material from the head surface... All you want to do is just clean the surfaces, not remove material. I believe you can also purchase Scotch Brite wheels for air tools if you need to remove heavy build up - just be careful as to how long you stay in a certain spot if using air tools.
I would also have a shop vac on hand to remove any/all particles afterwards from the piston holes, water jacket holes, etc... Thoroughly clean the block surfaces & cavities with the shop vac before installing any gaskets, etc...