I have an 06 Road King (standard model). Been riding for years but don't really know a lot about how they work and which upgrade does what. Right now it is totally stock. What would be the recommendation as far as exhaust, stage 1, air cleaner, hyperchargers (I'm not sure what they are), etc. Where do I start and exactly what advantage would the recommended upgrads do for my bike. What other upgrades would be recommended?

 

As you know,the basic things to change out first would be the air cleaner,exhaust(mufflers)and tuner.
There are so many choices and opinions it could make you confused.Try doing a search here and you will see what I mean!
If I was to tell you what to go with(brands),there will many other opinions that would not agree with mine.
One of the best things you can do is to check out bikes that have hadthese mods done.Talk to the owners,listen to the exhaust etc.