Ok..
The path between the 2 stages has some wood planks with a cart and toolbox behind it. I'm not sure if you're always able to go through them, but once I built a sentry behind the wall everyone was able to walk through and fall under the map.
http://img528.imageshack.us/my.php?image=plhaywoodbeta40000qg5.jpg
This door should be closed after the first stage, especially since people spawn facing it for the second stage. I'd suggest rotating those blue spawns for stage 2 as well.
http://img46.imageshack.us/my.php?image=plhaywoodbeta40001qx3.jpg
Not sure what this is all about. The effect is kind of cool having a grate over the red surface, but I'm pretty sure it's not what you intended.
http://img388.imageshack.us/my.php?image=plhaywoodbeta40002po1.jpg
In my opinion gates like this should move half up and half down instead of it all going one direction. If you take it in 1 direction, don't make it look like it's supposed to split in two.
http://img388.imageshack.us/my.php?image=plhaywoodbeta40003qa6.jpg
We didn't play a whole lot but the changes you've made from previous versions are very nice. You definitely need to close those blue spawn windows as noted by flubber. I'd also recommend working on your details inside buildings, especially on stage 2. The outdoor details are starting to look really nice, and you should keep going on them.
Someone also made note of your signs by the final red spawn. He counted at least 10 red arrows/signs pointing in various directions. I would recommend having a single arrow pointing right until the cart passes the spawn, then switch it to point left. Adding small "exit", "battlements", etc signs should help provide additional clues. If you need more clarity than that, it's probably a good sign that your spawn area is too complicated. IIRC, the map also had A/B signs, which should be changed to arrows since standard payload maps don't have A/B/C.
The timer for stage 1 is WAY too long. Yeah, it may allow people to cap that stage easier, but the better solution is increasing red's respawn times, not making them defend for 20 minutes. I'd say around 6 minutes per checkpoint should be the absolute max. A good rule is to start with lower timelimits far away from the final destination and higher timelimits close to it. That gives the defenders a bit of a chance to defend the early points.