First off good job in thinking thru the hand and trying to figure out what the villians would have done with different hands. Evaluating the players, action and the cards is essential in having poker instinct and from the sounds of it you're well on your way to developing that well.
I also struggled with trusting my gut for a period. Using a note book for pre game warm up I have a list of goals, motivations and reminders for myself... The biggest and boldest note to myself is "trust your instinct!"
This strategy of a pre game warm up I adopted from the mental game of Poker books
by Jared Tendler. I can not recommend these enough to players who are serious about improving their games.