I have painted posts and unpainted horizontal rails on the fence. Can I stain the rails after I install them or will the stain harm the painted posts

For the main deck, I would recommend a floor sander, similar to what's used for finishing hardwood floors. Put a 100-120-grit belt on it and take it back and forth along the deck in the same direction as the planks until you see bare wood. Once you have bare wood, I would apply whatever stain or sealant you want very quickly thereafter, as you have just removed a large portion of both the artificial and natural weather and bug resistance the wood had.

A handheld orbital or belt sander will get most of the stuff off the vertical components (handrails and pickets). You'll need a "corner cat" or other detail sander, or some elbow grease, to get the paint out of crevices and detail work.

You will not be able to avoid taking off some wood along with the paint. Paint (especially a product designed for this kind of outdoor application) will seep into the grain of the wood, and you will be removing wood before you see the color disappear and bare wood show through.

By the way, you will still need to maintain the deck after staining and sealing. The stain will last for quite a while, but you'll need to re-apply the water seal at least once a year, once every 6 months if you get a lot of rain.

You can definitely Zinsser over latex - just did it last week. Now will the Zinsser after latex not cover up the smell as much. I am not sure and not really sure anyone could say for sure but I would rather have it directly on the wood. Latex will sit and Zinsser will work its way in more.