Your map looks pretty insane, it wouldn't surprise me if you're pushing some entity limits.
But definitely sounds like a game logic problem if individual stages work.
Looking at the .vmf I can see you have two identical team_control_point entities.
Both have an index of 0 and have the display name "The Waterfall Bridge" (you have 4 points called this).
They're also unnamed so they can't be in any your round entities in the "control points in this round" field.
This also means they can't appear on the train_watcher HUD either.
Coordinates for the two control points are: 252 2606 102 and -655 3251 102
"The Lake Cave Stage" control point also has no name or unique index.
Coordinates for that point: 436 -1873 101
A lot of the blockbullets brushes you should definitely be deleted, it's destroying your vvis.
You don't need to playerclip blockbullets either, blockbullets stops everything.
But do use blockbullets2 instead of plain old blockbullets, better for optimisation.
Still, I do like the look of your map (I'd love to try it out once it's working) and I hope I helped you fix it!
Also your entire map is func_detailed. all of it. why.
[EDIT:] 91.4% on the entity limit! duuuude, too much!
Get rid of func_details and playerclipped blockbullets
I'm simultaneously impressed and terrified