Three given names, the second being my calling name: what to put on paper?
I would not base such a decision on the fact that it is funny or not, as funny depends by the person that reads.
Naming it is not a big issue as long as you are consistent during all your career. 
I would suggest you to pick up one of your three names, your surname and use the composition of them. As far as i understood, you are known as John Harris, so just go with this.

Cheers!