1 - Which of the already MFS filed returns do I amend in order to "zero out" the MFS returns and file a combined MFJ 1040X?

Either one.

2 - Do I use the taxpayer's or spouse's return as a starting document?

Either one.

3 - Does it make a difference which spouse is listed first on Form 1040X?

No.

This is the first one you have seen, but IRS sees thousands every month and will know what to do.