Just the name change alone is a significant problem with no easy solution... seems like his wife has had three different names? All it takes is one document to not match up properly at one point and the entire process comes to a halt.
I'm going through the I-129F myself as DIY, my Pinay has her first name misspelled on her current passport, we decided to get a new passport issued so that all the names match on all documents: BC, CENOMAR, Passport, vaccine records, police clearance reports, national ID card etc. so we could avoid any snags in the future.