Motorcycle Questions? Ask a Mechanic.
Hi Richard and welcome to the site, I’m Louie. Sorry you had to wait awhile but I’ll do my best to help.
Initially, the described issue almost always point to the battery and/or the cables and wiring pushing against the cover. The only corrective action would be to re-work on these parts so as to afford the battery side cover more free space and not have anything pushing against it.
Please post back with clear closeup pictures of the battery and the inside area covered by this "...battery side cover..." Click HERE.
It is my understanding that the cover is designed to contact/cover this screw head. Please click HERE.
Bear with me; can you please try with the taped harness above the red battery cable re-positioned a bit lower and the red cable to the starter relay pushed deeper?
Appreciate the additional information and earlier pictures.
Offhand and based on these, a possibility that comes to mind would be that whole metal portion holding the upper right grommet has bent out of position; i.e. ¼ deeper.
But then, not being there is a big disadvantage making everything from my end guess work.
Let me re-open the question in the hope of an alternate approach from another member oand/or a second opinion.
Still, good luck with the Yamaha.
Might also be worth checking comparing the new and old covers particularly the area that covers/touches the screw.
Sorry, none as it would appear that grinding would be the only available option/workaround.