"That" between "thought" and "could"
Is
It was me that Mr. Jones thought could do it.
correct?
Is that required between thought and could?
Solution 1:
I always thought only the references to inanimate objects use that or which, otherwise who should be used.
"It was me who Mr. Jones thought could do it." - sounds perfectly fine to me. ("Mr. Jones thought I could do it.")
P.S. I intended the text as a comment to an answer above, but cannot comment yet due to the reputation level.
Solution 2:
With a few more changes I think this is even more natural:
I was the one who Mr. Jones thought could do it.