Hi Nick, glad to see you are into homebrewing - that's is super cool. While I don't do it myself I do have a friend who has done it extensively. I've gotten quite a bit into local craft beer recently, and have considered brewing - but I doubt I'd want to invest the time.
Lots of options for an equipment closet. One would be to frame a false wall (with a false door on the right or left), moving your screen forward. One advantage of this is you could hide all sorts of acoustic treatment behind it with no need to make it look publicly acceptable (same with cabling runs etc). For example you could SuperChunk both corners, and place your equipment just inboard of that. This solution also makes it easier to deal with your game consoles, and all of your cable runs can be short except those to the projector and speaker cables to the surrounds, which seems pretty convenient (those are relatively stable in technological terms, for the PJ just run HDMI/component/composite/S and you should be done for a good long time - though large conduits are always a good idea). One problem is that you would need to move your door backward, risking getting into the area you want to put the Bowler. You'd need to revise the drawings to do a good job evaluating this. Also, I haven't exactly reviewed a lot of the build threads so I don't think I probably have that many ideas compared to those more experienced.
Studiotips Superchunk: http://forum.studiotips.com/viewtopic.php?t=535
Another option would be to build an equipment and media closet in one side of the rear of the room. This has the advantage of not threatening the the bowler space (and providing you somewhere to put your media) but will make dealing with the game consoles a hassle.
Are the seats to scale in your image of the theatre? If so, then your room is a LOT larger than mine (which is a good deal, really). One thing I think is that for better acoustics you need to pull your seats all forward so the rear row is farther from the rear wall. Do you have a planned screen size yet? Knowing that will help you figure the viewing angles to know where good seating locations are for different resolution material, and you need to know that to calculate sight lines for your riser(s). Easily done with the calculator here: http://www.theater-calc.com/
Also having an approximate screen size would help you plan for where you want to mount the projector by considering projectors in the technology/price class you'd intend to buy - note that projectors' image quality is better in certain zoom ranges. Your room looks long enough that you'll definitely need a hush box, which is going to steal some height from the ceiling somewhere in the room. With the ceiling height you have, I think you can get away with a reasonable height riser and could easily have a bar-height seating third row like the one I showed you in the other thread. I'm 5'10" and in bar height seating my head is roughly the same position as when I am standing - and since the seats aren't on a riser you don't have to provide clearance for someone to step up.
I can't clearly read the size you have laid out for the room, but it sounds like you also have enough data to run the room through a room mode calculator to get an idea of how much acoustical work you will have ahead of you, or be able to make few-inch adjustments now to avoid more work later. http://www.bobgolds.com/Mode/RoomModes.htm
I'm not sure how good it is for making layouts of things, but the riser I showed you was designed in Google Sketchup. There's an extensive library of architectural features/furniture/etc (I didn't model the sofa and chairs and switches and lights!), though I'm new enough to it to not know if it's any good at creating layouts to build from. The price is right: free.