I think you are right about the note indicating it was a researched crime and not a random one.
The $118,000 was not a cash bonus, but a stock option that was given as a bonus 10 months prior. It's current value at the time of the murder was roughly rounded to $118,000.
Stock option bonuses are a matter of public record so this indicates someone with a desire to know about the Ramseys. If the Ramseys wrote the note to throw suspicion off themselves I think it would have been very short and generic instead of rambling, personal and strange.
But if it was an intruder, he felt comfortable enough inside the home to tear up two drafts of the letter, then pen a three-page missive, taking it back upstairs to leave it on the stairway - all risking the chance that he would be caught or would leave incriminating evidence. Almost anyone who is skilled at committing a crime knows to get the heck out of dodge as fast as possible rather than staying around to pen a long note.
My theory all along is that the Ramseys are hiding something about that night - maybe not that they were the killers but that they know who it was. If my child was murdered in my home, I would be pounding on the door of the police and the sheriff demanding justice until the killer was caught and then I'd be at the trial every day to see that the fiend was put away. My instinct would not be to lawyer up, hire a PR firm and then play keep-away from law enforcement. A large amount of the animosity towards the Ramseys from LE and the media they brought upon themselves because they became defensive after their child's death instead of taking the offensive and demanding justice like most parents would do.