Regarding fortifications, I'll be a little more explicit. A tournament has more stringent guidelines than casual play, and adding terrain can have a major impact on how the battle will play out. For the time being, you should keep your custom models close to the official ones in terms of size and layout. Changing the aesthetics is fine, but moving things around for in-game advantage is dancing very close to the line, and I'd rather we just avoid it. So, to address your specific questions:
"How close do the size and shape of a homebuilt bastion need to be to the imperial model?" As close as possible.
"Do the heavy bolters actually HAVE to be arranged in a perfect square?" Yes.
"Can we make Bastions with a different layout of access points?" No.
"Can we make Bastions with a different layout of fire points?" No.
"What's the arc of fire on those heavy bolters?" They appear to be the equivalent of hull-mounted weapons, which means a 45-degree arc of fire.
I would argue the heavy bolters on a bastion actually are sponsons, and have a 90 degree arc. In this way, they are very similar to the corner weapons on a Monolith -- all points in the circle are under coverage of at least one heavy bolter, and the only way you'd get two bolters to target the same target is to have the "border" between two quadrants pointed at a particular unit. Because a Bastion can't rotate the way a Monolith can, this is actually much more limiting.
At the same time, there are no "dead zones" around the bastion. As I understand it, a hull mounted, 45 degree arc would cause this, Sam.
For access points, it is simple, a Bastion has precisely one. It doesn't really matter what face.
Fire points get a lot more complicated, as you CAN model it different ways on the standard kit. On the "mid-level" (top-level is the battlements) two faces have two firepoints, and two have none. On the bottom level, each face has one, EXCEPT the face with the access point (you glue that over the slot). So MY Bastion has one face with 3 slots, 2 with 1, and 1 with 2 (and an access point) but it Could have been 2 with 3, 1 with 1, and 1 with none, for instance.
Also keep in mind two guns can fire out of each slot, so it's really 6, 4, 2, etc.