I'm liking the changes. Stage 2 and stage 3 are looking better.
Health/ammo:
One big thing I'm noticing is your ammo/health distribution needs a lot of work. There are far too many ammo packs and health packs everywhere. This especially unfavorably benefits spy. Think about a red spy going from spawn towards blue team, and he can pick up ammo everywhere without ever having to decloak, and when spotted, can find ammo again just as easily.
As for health packs, a generally good place to put them is in fallback areas. Imagine you are fighting in a battle and you are low on health. Where do you go? you retreat to the backlines to look for health.
Another example is on your stage 2 first point. You have health/and ammo packs on the high ground where only red can access them. imo, they shouldn't have that much ammo/health AND the advantageous high ground along with perfect cubbies. they should have to go back to lower ground to get their ammo/health and retreat off of their advantageous spot. At the most 1 full ammo pack up there, but definitely not 2. No health up there.
there are some gameplay things as well, but I'd like to try the new layout before I make any comments.
keep up the good work