FWIW this Vikings fan's (and lawyer's) take, after reading the report and much of the last 20 pages above:
1. Yes, the balls were likely intentionally deflated and likely intentionally deflated by McNally in the bathroom, as found by Wells. Ie the information in the report, including the text messages, and the disproportionate drop in PSI in the Pats balls vs. the Colts', suggests intentional deflation. The case that the Wells report is absurd, incompetent etc has not been made out IMO.
2. It does seem unlikely that McNally would do this on his own volition without express or implied consent from Brady, likely thru/with JJ.
3. This is not trivial misconduct. If one team's equipment guy got unauthorized access to, and altered, baseballs after the umps rubbed them up, for the purpose of helping his team's pitchers, for eg, this would be acknolwedged as a significant breach IMO. No, the ball tampering did not affect the result of the game but I am not sure that matters much except tothe pride of Pats fans.
4. There are plausible conspiratorial angles, which could operate independently or in combination:
a. Brady was set up by McNally -- who (on this theory) was pissed at Brady for one reason or another, and deflated the balls lower than Brady's preferred 12.5 knowing or suspecting that this would be found out. "I will give him a fucking balloon..Fuck Tom...where are my new kicks etc"
b. The Pats were set up by the NFL. Knowing or suspecting that the Pats had a practice of post-inspection deflation, they allowed McNally unfettered access to the footballs before the game, knowing or suspecting him to be the deflator, despite being warned by Colts of a concern re this precise issue. I do struggle with how the meticulous Anderson et al could lose custody of the balls pre-game given the prior warning. The "evidence" relating to concerns about the radical over-inflation to 16 PSI (by the refs?!) in the Jets game suggests that there may be much more going on here.
5. If the Wells report finding is broadly accurate, then McNally and Jastremski very well may be in a position to ruin Brady's reputation by singing. Hence if Brady (and his reps) dont speak ill of either that could be seen as supportive (to some minimal extent, I think) of the accuracy of the Wells report. Ie one obvious Brady defense to this, already advanced in part, is: "I like 12.5. I dont want anything done to them after that...and if that stupid SOB McNally fucked with them to bring them under 12.5, I am pissed, he should be flayed." If we don't hear the second anti-Mcnally part of that defense, that suggests to me that Brady is afraid of McNally.