Ok, as requested I did those screenshots and drawings. It was harder than the drawings I did for youme, and probably less useful, since I still believe the forward spawns reduce the need for forward engineer bases. I also struggled since there are some areas that are pretty much perfect that don't get used because there's better strategic (or more fitting in the flow) positions nearby. So it's not so much changing that location as changing the other nearby location. I focused on the areas you requested...
This first area is tough, since I like a lot of it, but you're right about that building not getting used much. I think this is mostly a result of the spawn being so close to CP1, where there's no need for a forward base. Nobody's going to wait for a teleporter when they can walk 5 seconds and get to the same spot. Same for ubers... why risk building somewhere out in the map when you can build them at the spawn and be 100% safe. Think about Badwater... it's rare that engineers will set up until after CP1. I do it once in a while on the ledge, just to keep pushing back and damaging the enemy, but it's usually more useful if I try building up to CP2.
Anyway, the problem here is that by the time the train reaches 1, it's easier for the attackers to just use the green paths and force the train through than to take the red path. This will change once red wises up and loads this area with sentries, though. Another problem is that it's very hard to build that room with the 1-way door because enemies can too easily loop through the back ramp and/or spam through the upper doorway. I want a protected area for my sentries if I'm going to build them. To do this you could move the upper door back on the building, which would reduce spam in the forward section. I might be wrong about where that door is, so maybe I'm thinking of spam coming through the window. Closing the window and making it transparent is another option, which would force the room to be used for building ubers. You could also remove the rear ramp/doorway and change it so they have to move through the corner building from that round rocky area. That would flow more naturally into that area and make it harder for defenders to get in.
This area is a real pain in the butt for trying to give advice.

Once again, the spawn is so close to CP2 that there's absolutely no need for a forward base. Engineers are relegated to putting up sentries and dispensers for area denial rather than forward bases. Right now the most likely spot for me to build would be at #2 since it's pretty protected. To force people to use the building more, #3 still needs to be more risky. However, that's also a risk since it's such a long path of track. To keep it from getting too defensible, and to add some more height to the area, you could increase the building at #6. Making it a 2 story building where soldiers/snipers could overlook #3 would be fun.
The area by 4 will never get used because right now it's useless. It gets unlocked when CP2 gets passed. Unfortunately the direction of gameplay at that point switches in the complete opposite direction. Instead of trying to build that area, people will hug the near wall and push up through the rounded corner. This area would be far more useful if CP2 were pushed up the hill and that back hall always remained open. That would make it an ideal spot for the attackers to make a push at CP2. It needs some more protection by the entrance, which I'll cover next.
Right now #5 is a complete spam trap and perfect sniper target. You can simplify this area to get people to use that building more by removing that corner area and widening the side door. The lower inside section would need a little reworking as well. People avoid complicated areas of maps, so keeping it simple will make it more likely it'll get used. You still have 3 routes through and this would help protect the back hall some more, so it might be worth it.
This details the inside with some possible changes. You can see the spam trap area and the sniper up the hill with the perfect shot through both sides. It's a spam trap since it's an enclosed area lower than the surrounding area, with one or more easy spots to throw nades through. By expanding that yellow brush you protect the main path up. I'd recommend trying to add another stairway up in this area, even if it's just some boxes that can be jumped up on the other side. Spies will thank you. On the other side the entrance to that side hall is completely exposed to the hill. Adding some protection here would help. I'd also suggest removing one of the entrances, since it'll be easier for teams to spy check when building in there. The ledge is expanded as well, since right now a single demoman could put 2 stickies right at the corner and knock off any blu running through. By widening that ledge they can avoid that corner a bit and have some more protection.
This is the area I absolutely love, but there's no reason to use it right now. The spawn is right around the corner, so attackers only need to walk the green path to be to the same spot. A person is more likely to walk 8 seconds to get to the same point than to wait up to 10 seconds to teleport into a blind area. The single best solution I can recommend is moving that spawn to the room down the hill. To make that area with the 1-way gate more useful, you should narrow out the path under that overpass a bit. Remove the part by the rounded corner and narrow the track section, which will force people to go around. Another issue here is that I'm still far more likely to build where I circled, since defenders normally come through in this area. I don't see that as big of a deal though since once you get 2 engineers they'll spread out and build in both spots.
I won't mention changes at the end, since I love the changes you made. I'd possibly recommend a 1-way door on the new path behind there, which would allow a sentry to defend a teleporter exit in there. Putting the 1-way door right where the tunnel exits (in the room with the ramp going up and the health/metal in there) would be fun, since an engineer could build his sentry behind the door and open it when he wanted it to shoot at people. >

The drawback (and there should be one) is that it's so narrow that he can't build it back, which means demomen can destroy it easily with stickies.
Overall I think the quantity of forward spawns is really hurting your map, but hopefully these changes will help. I'd make a single forward spawn, at the bottom of the hill between checkpoints 1 and 2. Or in the warehouse, which would obviously get it used more. Award that forward spawn once checkpoint 2 is reached, and move cp2 up to the top of the hill. Since the section between checkpoints 1 and 2 is the least played right now, expanding it out should give it more playtime compared to the other sections. It would also make engineers a commodity on offense, and make some good forward base areas that could stay between checkpoint captures.
I know I'm stuck on the whole forward spawn thing, but I hope this was still helpful.
