My question is, if I decide to take the train into the UK not to avoid any steps because I know that is not possible, will she be able to fly as my carry-on again instead of as excess baggage? Or does that ruin her quarantine process? Example; flew direct SFO to CDG(paris) as my carry-on and took the eurostar into London. Is that do-able or am I being completely rediculous?
I'm not sure about carry-on. I looked into it for my cat and dog and had the option to fly them as "excess baggage" (basically the exact same thing as if she went cargo, but at 1/10th the price). I think carry-on for pets is being phased out (because the crates required are
tiny), but I don't think DEFRA cares how the kitty gets to France as long as she comes in from France the correct way.
Looking at DEFRA's site, though, the only approved rail route from France is Calais -> Folkstone, so you can't take the EuroStar from Paris. You'd need to look into that further. (My plan was to fly to Paris, train to Calais, ferry to Dover, train to London, FWIW.)
Are there any advantages to her having a passport now?
Definitely. Assuming that her rabies has been kept up-to-date, that counts as all her documentation. Come to think of it, if her rabies is up-to-date you may be able to skip the 6-month quarantine altogether, since she has the proper documentation already. I'd call DEFRA and ask. (I know if I took my pets to the US for a visit and came back, they wouldn't need a quarantine, but they've already been approved to come into the UK.)
Also, are most vets USDA certified? To double check, just find the USDA number and call and give the details of the vets?
I think most are, but yes, just call and give the vet's details. Make sure to identify the person - my local vet practice had 4 vets but only one of them was certified.
This may be a stupid question as well, but when she is quarantined that means no going outside, right? Not even on my balcony?
Assuming you mean the at-home part, no. My cat and dog lived their normal lives for 6 months at my house.

The 6-month wait is purely to make sure they don't contract rabies (as its incubation period is 6 months, so they could've been bitten by a rabid animal 5 minutes before vaccination and still become rabid 5 months and 29 days later).
Good luck!