Hmmmmm...... You ask an awful lot to be considered here. However, let me make a few suggestions:
The ceiling shape is fine and actually helpful. However, if you're wanting to contol some audio anomolies, think of putting some acoustic treatments on the side walls. You can make these yourself. Use about a 4X2 panel, approx. 2" thick, filled with rockwool. Place these on either side of the room, about 4 - 6 feet from your speakers. They should be about 2.5feet off the floor to the bottom edge.
Next, have two more of these panels at the very back of the room, about 3 feet in from either side. This is a basic minimum and is used to reduce "reflections".
About speaker placement, the center channel will be fine. However, try to find a way to direct the speaker down to the front row. This way you won't loose the quaility of sound that comes from the center of the cone. The left and right speaker should be lowered to achieve the same thing. They should also be as close to either side of your screen as possible. Otherwise, your sound coming from the front will be too wide. Since you are having to build the cabinet anyway, try to find a way to incorporate the left and right speakers into the cabinet, on the center level of the screen.
Your side speakers, again, should be at about the level you are sitting at for your ears. However, your furniture should not be against the walls, next to the speakers.
If you can afford a 7.1 or 7.2 system, this will be your rear speakers. Again, check the height of your placement. Remember, you will be sitting down in your room. The audio coming from the center of the cones is the best. If the cones are to high, are over your head, you will loose much of the response from those speakers.
Subs are non-directional. You can place the sub nearly anywhere up front. Of course, if you use a good sub, you will want it to face toward you. This will assist some in the "pressurization" from the sub. You will need all doors and windows closed to get the maximum effect from your audio.
Also, for either a 7.1/2 or 5.1/2 system, you will need a good processor. Otherwise, you've just wasted your money. The big box stores will not be able to help you much here. You need to go to a true audio professional. It will cost more, but you will be happier with the end result.
Ventilation: I don't see that you're going to need fans. You're not going to have that much equipment in there. Just be cautious about "stacking" equipment. Leave the back open if possible. If not, maybe a 4 inch gap at the top of the bottom shelf along the back. This won't be seen unless you're crawling on the floor.
I hope some of this helped. You can visit our official site at www.advancedaudiovideo.com
for more ideas on planning and building a home theater. There's plenty of pages there with information to help you .