to guess what is the tool he has carried out the crime with
I'd change the position of 'is' as it's an embedded question and say:
to guess what the tool he has carried out the crime with is
If you think it's too far removed from the word 'tool', you could do it as follows:
to guess what the tool is which he carried the murder out with.
I've got to go out, but I'll be back in a bit and add some more comments if they're any use.
