you can confirm if peaks are true or fake from cost down test.
A. At slow roll check if these peaks remains there or not. if yes then they are not real. B. You can check the total energy from these peaks during cost down. if it is constant then they are not real.
Regarding the gap, if your on line system doesn't keep trends of the gap values then it is better for you in the future to collect it as a routine job by your data collector. this is a super critical parameter for a condition monitoring guy.
To confirm your doubts about misalignment, try to draw the shaft center line plot within the clearance circle at each bearing (especially across the coupling). this will show you if any abnormal SCl location is there or not. it will more clue about misalignment.