My guess is booster. I've experienced similar troubles the whole time I've owned my current car. I've bled and re-bled the system, had it power bled, replaced lines, replaced and rebuilt all calipers, and replaced the master cylinder with no noticeable effect.
It wasn't until I borrowed a booster canister off a mate's GTR that they started working properly.
I've now replaced the booster, haven't had the opportunity to even start it yet to see if it's made any difference yet...