Unfortunately with countries where some applicants have committed fraudulent behavior many of us genuine applicants end up paying the price . I speak as someone who had no red flags but we were delayed by our lawyers incompetence w paperwork (and just poor luck)
The basic fact is for some reason there appears to be a suspicion as to whether there is a genuine relationship , or someone taking advantage of another. The paperwork snafu is common enough in developing countries , but has been flagged as possible evidence of fraud. The NADRA stuff has got to be sorted out and probably has been. I think the real challenge is providing a lot of evidence of a real relationship. Being able to speak each others ( or at least a common) language should help.
IM not a big fan of lawyers but I think in this case they should be able to help you not make paperwork errors ( as has happened) and maybe guide you on evidence you may need to prove the truth