As others have stated use wire wheel on drill after removing everything you can and then taping all the holes. Then wipe down with paint thinner, spray (aerosol can) with whatever brand of rust converter you can find locally. This will kill the rust you cannot remove and forms a good base for the paint to stick to. After that dries, use dupli-color or other brand of engine paint.
To make it look very nice for very little$ take all your bolts and wire wheel them., Just hold them one at a time with vice-grips and hold them up to a wire wheel on a bench grinder. It will clean them very well. Then very lightly spray the bolts with the rust converter and then spray with a detailing paint such as Eastwoods products. You can use semi-gloss black, dull silver, spray grey, detail grey etc. It makes the whole engine look fresh and better than new. It takes very little money a little work but is well worth it. Big difference between an engine that looks like it came out of an old car vs. one that looks better than new.
John