Morning
@motopoeta . I would look at the earth/ground connection as the likely culprit. The positive terminals are ‘designed’ as such and any bolt you use as an Earth/ground connection unless it is a designated Earth/ground is really just a ‘compromised’ one, especially if it is being snagged. If memory serves me correctly I used a larger ring tongue terminal and bent it slightly downwards to stop the seat snagging it. There is a designated raised ground stud at the rear of the right hand cylinder head on the engine if you fancy running the cable there without having to strip anything out for access. It was the one I intended to use when I first researched fitting the pigtail.
Edit Afterthought: I am unaware of how the Thunderbox is supposed to be wired but the positive terminals under the seat are permanently powered, does the Thunderbox need to be powered from ‘an ignition sourced live’ I am wondering perhaps? Good luck with it! Either of the two theories above ‘could be’ the cause.