If he has one 2 toughness monster token, can he spend only one toughness as clue token? Then does he still keep the monster token?

I think it's one trophy = one clue, not one toughness = one clue, so a two-toughness monster is no different than a one-toughness monster for the purpose of the Secrets of the Dead ability.

Zeah, Thomas is right:

"Secrets of the Dead - Any Phase: William may spend his monster trophies as though they were Clue tokens, on a 1-for-1 basis."

The kez-word here is "monter trophies". Nowhere is referred to toughness. Clearly, you may prefer using the toughest one in some different ways, but still, William ability is good