1) For general use, aim to fully illuminate a 0.5" diameter field. That literally means that the light from the entire primary will reach a 0.5" diameter circle placed at the focal plane, and thus all objects imaged in it will be fully illuminated. This also means that the edge of the secondary and the bevel will not be used when viewing small bright objects on axis (in the center of the field), such as planets. Planets require good optics, and the edge of a secondary mirror is often rolled off, and there is a special risk on dielectric-coated secondaries, as the coating itself can stress the glass.
    Also, the bevel on the mirror can have some aluminum on it, and this is very effective at causing ghost images and scattered light. Additionally, the bevel is included in the optical diameter, so some surface is lost to it, and some secondary holders cover the very outer part of the seconary in order to retain the mirror in the holder, so that area is lost too. The lost area means an effectively smaller secondary than the quoted size.
    A 0.5"-diameter field will provide enough light to illuminate most eyepieces. The widest field eyepieces have field stops that are larger than this, but in short focal ratio telescopes the falloff in brightness near the edge of the field will be difficult to see. In longer focal ratio telescopes the falloff may be noticeable in the widest field eyepieces.
    For strictly planetary use or very high magnification lunar viewing, you have the option to choose 0.25" size or slightly smaller. Vignetting may be especially noticeable when using low-magnification, wide field eyepieces in a telescope with a high focal ratio. But, by choosing a small diagonal, you're deciding that the telescope is not for wide-field viewing. Make sure your secondary size is at absolute minimum 1/8" larger than the size for a 0.00" field, and 1/4" to 1/2" larger for large fast telescopes.  A 0.00" field only fully illuminates a star at the very center of the field, and the lip that retains the secondary and blocks part of its surface may cause you to not get light from the outer part of the primary mirror. Also, secondaries can have rolled edges too, so it is smart to oversize them by a bit.

2) If you can notice a 3% change in the central obstruction (secondary mirror diameter / primary mirror diameter * 100), then you are either crazy or a far better observer than I am! So, I recommend choosing the slightly larger secondary if there is any question as to whether your secondary is large enough, especially if you have decided to only try to fully illuminate a small part of the field (~0.1"). With this small field, the mechanical centering error of the secondary may put it outside the cone of light from the primary. Give yourself some wiggle room!

3) Where do you put the focal plane so your eyepieces focus? I like to place it ~0.6" (edited) above the top of the fully racked-in focuser. Depending on your eyepieces, you might adjust this slightly, but it works for me. This allows in-travel for a Paracorr and possibly a barlow lens. So, the variable d2 below is the distance from the center of the secondary mirror (center of the telescope tube) to the focal plane, which is just above the racked-in focuser.

Table of Secondary Mirror Sizes for Visual Newtonian Telescopes

Secondary Offset