That's why I recommended the thread chaser, it makes it easier, but having some carb cleaner, and compressed air on hand helps. I bought a little hot dog compressor from Home Depot just for this job, it is not for running air tools but is great for cleaning parts, airing up trailer tires, etc.
After you're done cleaning up both the bolt holes and the bolts themselves, make sure the bolts all thread in all the way.
PS, I used Permatex Aviation, used about a half bottle on that part of the job! The OMC Shop Manual I have recommends OMC gasket sealer which is the same thing as Merc Perfect seal if you have any of that lying around. The Permatex Aviation is similar but not identical.