The first is the prohibition against foreign contributions to U.S. election campaigns, which you've cited correctly there. The case against Trump Jr. in this regard is very weak (or non-existent) because that law could not consider most forms of information to be a "thing of value" by any stretch (i.e., it's not a published work with a dollar value, or information subject to copyright that is worth a lot of money to the holder of the copyright).
The issue the judge seems to be addressing is the legal requirement for anyone applying for security clearance to report their contacts with foreign governments and government representatives (not unaffiliated individuals, to the best of my knowledge).
I agree that the first amendment protects the transmission of information as “not something of value”. This phrase is intended to refer to money or a quid pro quo. As far as we know nothing changed hands and no payment was made. This can get confusing in a campaign as the payment may be a favorable position later after the election (Something Hillary is suggested of offering via her foundation.)
Usually the Judge knows his law, but in this case I believe he has fallen in with the opposition.
As to the security clearance form, the form is confusing and demanding and can require long hours of research to determine what meetings were attended, what clubs and movements were attended or joined. Jared can probably be excused to some degree for not getting detailed lists correctly the first or second time. The FBI can usually be trusted to assist in getting what they want, it does not have to be adversarial until they find you are deliberately hiding something. But the penalty here would be lying to the FBI.