You didn't indicate what state (unless it is buried in there somewhere rather than being in the first line as the site prompted you).
It's not harassment and since you were not moving, what you have here is called a consensual stop and the officer doesn't need probable cause or even an articulable reasonable suspicion that a crime has occurred. He's free to ask you questions based on his own hunches.
You're not getting convicted based on the "sworn affidavit," that's only information needed to bring the charges. In addition, even if there are errors, it's not a "get out of jail free" card. They can be corrected during the process. This information will not be used at trial (it's inamissible actually in most states).
The answer to all parts of your third question is "no." They don't need to give you receipts. They don't need to charge you with every violation they find. They can charge you later on if they feel there is probable cause to do so.
As Mr. Free9 says you need to get serious help with your substance abuse problems and you need a lawyer for your legal problems. In many states, what you've lsited is a felony level charge. Even misdemeanors are nothing to sneeze at.

