What is the best way to stop the corrosion and/or replace bolts/shafts?

The best way to stop it is to get it out of the rust belt. I live in on the east coast and deal with this all the time. Once it is out of that environment it will slow down and if you are in a place like AZ, it may even stop where it is. With that being the case, I would go the next step and if you have no issues with the vehicle such as leaks I would under coat the under carriage. This will encase the components and stop the rust from progressing. However, the manifolds cannot be coated. So if they are not leaking, I would not replace them as you may break the studs and if that is the case and you can't get them out you will need to remove the heads. So again, if there is no issue, let it be.

There are a ton of products out there but one that I have heard good things on recently is called Rust Bullet. I am pretty sure this is a professional installation as you will need a paint sprayer but it sounds like it goes on evenly and coats pretty well.

If this doesn't look appealing, then just go with stuff from the local parts stores. Let me know if you have questions. Thanks

Yes. Please keep us updated. I totally understand the fear of wanted to touch rusted bolts. Pull one set of heads off to extract the bolt and you learn the hard way to not touch them until you have too. Thanks for the update.