Sorry for your loss. I am late to this post but here's my 2 cents.
The yellow spots - can that be velvet? Velvet is supposed to show up as fine dust like yellow spots. The ones on the pics might be too big. however, the active swimming (flashing like behavior in not too free swimming fish?) & external spots would point to an external parasite of some sort.
If it is velvet, you might consider treating the whole tank as it is very contagious.