I strongly advise you to get used to doing normal (or fast) compiles every now and then. I believe you would've spotted this problem much earlier if you had done so.
Well, after taking a quick look at the map, I can see some troubled things that greatly increase the compile difficulty. I haven't compiled myself, but these are things I learned over time to keep compile times down and work more tidy.
1. Take those hills for example. They're nice, but cause a lot of extra work for the VIS process. Make them func_walls to ease this process - the same goes for cylinders and other small or complex brushes (like all of that arty statue). Unless these objects hide other area's behind them (as in, a great wall or building or such) or are used to seal off the map, such objects are best made a func_wall. In case of cylinders this also saves you some polygons in-game.
2. The 'splintered' arch somewhere in the lower left corner of the map. Horrible brush-work, I assume it's caused by carving (evil tool when used with cylinders). Use the arch shape instead. It's best to avoid brushes to overlap each other too, maps quickly become hard to work with otherwise.
3. Not really something that will optimize compile times, but certainly will be helpfull along the way (to prevent leaks to occur and to make handling larger maps easier) is to stick to the grid. The larger, rough architecture is best kept at the grid lines so you can make sure there are no leaks and then putting in the details with smaller grid sizes can safely be done.
4. The use of sky brushes is sloppy. You put one brush on top of it all but there's still a lot of area's connected to each other where that isn't needed. Put more sky-brushes on top of those low buildings to divide the map into more smaller area's, and try to minimize the visibility between those area's for performance sake.
As for compiling through Hammer, there are tutorials here to help you set it up correctly. Batch compiling works fine too, though, so that's a matter of taste.
As for the map itself, the first thing that strikes me are the horribly long corridors. I'm sure those will not be good for gameplay... the plaza at the CT start looks nice, with some interesting use of height difference and such. Overall, most area's are probably too large and lack cover. I haven't playtested myself and I'm not a die-hard CS player, so I can't go into much detail here, but these are quite general rules for fast gameplay.