If I have 5 perception and I pick the Four Eyes Trait would that count as having 6 perception for the requirement for Sniper/Better Criticals or would I need to have 6 perception before I pick the Four Eyes Trait.

The latter. The added bonus of your glasses won't let you pick perks like that.

No, temporary item buffs do not count during the level up process.

It's actually slightly worse than that (iirc from my four eyes character) - if your PER is 5 and you take four eyes it lowers your base PER to 4, and wearing glasses gives you a +2 item bonus taking it to 6. However it is your base PER (which is now 4) that is measured for perk requirements. So choose your stats carefully if you want to take any perks later on that require higher PER.

ETA: Just in case you didn't realise, you can only take four eyes trait at level 1.

You need to have 7 PE (An oversight, they should apply a constant -1 PE effect with no glasses instead of - 1 base PE) due to the way the trait designed

Yeah, kind of a bummer how it's implemented. A logical RP build is a scientist/energy weapons character with Four Eyes, which would do best with a bunch of perks requiring high PE, so you end up with 9 PE after putting on glasses and a hat, which is way more than you need ... but any less than that and you can't get things like Better Criticals.

Really? [tantrum]

I wish I had known that before starting my current run-through.

(Begins pondering how to quickly rack up a pile of money and the odds on sneaking all the way to the outskirts of Vegas to see "you know who" for an upgrade... at level 3) Hmmmm....
Along with skipping a useful perk and instead boosting my stat at the next level up. What a waste. (sniff)

Thank you for the timely post. (even though it shows that I wasn't paying attention when setting up my newest courier)