The Torx bolt in question is just a bracket fitting and the bolt in the centre of the tri plug just a blocking off bolt for access so as nothing of any consequence has been touched you are going to have to go back to basic principles and put down the change in starting characteristics after those fittings were touched as being coincidental, that sort of thing happens all the time and really messes with your mind!

Marking of the bolt in yellow tends to be used as anti tamper evidence but we use it as "torque conformation" to show that the particular fastener in question has been tightened to the correct specification, this aids quality control and precludes having to go around checking everything as if it is loose the paint will show it is moving. We also call it Gimp paint....long story.....

You need to go back to the beginning now ignoring all that has gone before so starting with a code read and then a COI check.