Placement of "that".

Where would you place the "that", and why?

1. "The trouble is, in the sentences first quoted, that the main subject of the sentence is not the same word that would be the subject of the participle, if this were expanded into a verb."


2. "The trouble is that, in the sentences first quoted, the main subject of the sentence is not the same word that would be the subject of the participle, if this were expanded into a verb."

NB

The BNC shows 153 per 1 million words for "the trouble is that" and 143 per 1 million words for "the trouble is,".

http://corpus.byu.edu/bnc/x.asp

#2 sounds better (US English).

How about just avoiding the problem entirely:

3. "In the sentences first quoted, the trouble is that the main subject of the sentence is not the same word that would be the subject of the participle, if this were expanded into a verb."

or even:

4. "The trouble in the sentences first quoted is that the main subject of the sentence is not the same word that would be the subject of the participle, if this were expanded into a verb."