A few of those can be explained away.
One of the easiest explaination would be that Starfleet doesn't keep very good records, so that Picard couldn't have found out about the Borg, even though Archer had previously encountered them.
* The galactic boundary thing is kind of strangely depicted in Star Trek. In one case, it's the edge of the galaxy and in another it's the center?
* Although the age of Chekov doesn't bother me, I do find it kind of silly how the writer didn't bother to look up his age in TOS. Given how he's only 4 years off... very close. Why not be right on target, right? The effort to check it would've taken only a few minutes.
* I do agree that the Klingon D-7 design went through numerous upgrades over time. There is "official" retirement, but then there's time when you pull everything out of mothballs for an all-out war; every ship becomes valuable, even the retired ones (if they can be retrofitted for service).
* With an enemy as powerful as the Borg, I'd find it unconscionable for Starfleet not to keep very good records on them! The simplest explanation is that it's a timeline error. ENT "revised" a number of previously established "future" events.
* The torpedo gaff in VOY was one of the more glaring ones... although, remember it's just one line in one episode, not something that is emphasized repeatedly. So, I like to chalk it up to "writer's blunder" and continue with the assumption that they can manufacture replacement photon torpedoes periodically on their own.
* I can forgive the time calculation based on light years. We didn't see a solid formula presented in TOS, where multiple calculations were presented in several different episodes that all followed the same formula. I think we saw some disparities even in TNG. Even within VOY, there were some inconsistencies. But, as long as it's "background" info that is only momentarily presented and not lingered on, it's not a big deal IMHO.