But the Wells report might be exactly what the NFL wanted. They may have wanted a plausible, professional, report, with enough pseudo-scientific shit to give it a sheen of "complexity" that would confound, or bore, most people and the strident minority that bothered to write an equally confounding and boring rebuttal could be written off as self-interested and suspect.
It's the same playbook that cigarette companies and global warming deniers (and most conspiracy theorists) use(d) for years.
I mean, yes, the report is bullshit and contains lots of bad science. Of course it does, because it needs to to come to its final conclusion. They could not have given the NFL what it wanted without the very "shoddiness" you cite as being flaws.
If your firm did the report in a way that was more thoughtful, honest, and thorough (and I have no doubt they could have) the NFL would have told your partners to stick it.