In thr season 4 finale the one where jane fakes like he killed lisbon and rigsby there isna HUGE clue.
Well maybe its a small clue.
When that lady darci goes to the morgue to check up on the bodies
She discovers rigsbys is obviously fake.
There is a very distinct i think yellow toe tag on the sureagates toe.

***The exact type of toe tag was on the bike that red john provided for jane to ride to meet him.
Check it out for yourselves.
Its draped on the front of the bike.

Conclude whatever u want but this was one of many clues for me.