Some of our more skilled practitioners of organ playing will no doubt contribute more eloquently, but meantime, here's my tuppence worth:
Stop choice can be indicated, but as no two organs are alike its always going to be a compromise. Often giving an idea is best, eg "soft 4' flute", "8' reed", "strings", "full organ with reeds", "sw celeste, gt 8' diapason, sw to pd". The organist will draw whatever best approximates this on the instrument to hand.
If you specify stops exactly, organists will adjust to what they have available anyway. There is such a vast array
of stops and names that its extremely unlikely that my instrument will have the exact specifications you have called for when arranging for yours. Its also worth remembering that your diapason might not sound a bit like my diapason!
Pedal range as written on the page stops at the C on the 2nd ledger line below the stave. Nothing is ever written lower than that, but a 16' stop will give you an octave lower (almost all organs have 16' in the pedals, and this tends to be the 'default stop' in the pedal line- the 'octave down' is taken as read) and a 32' stop an octave below that. I've never seen an 8vb marking on an organ score. If you want the 32' stop out, best to specify it, but bear in mind that such a beast is usually only available on a bigger instrument.
Not all pedal boards have the same compass either- some go up to G above middle C, some only to F. Embarrasing when you haven't noticed and try to play the casing!
Dynamics can be useful. We will try and interpret mf, p, etc, but changing stops will change tone quality as well as volume, and no organist will thank you for expecting them to be an octopus, managing a stop change a bar whilst playing semiquavers in both hands and feet! Don't forget the swell manual is enclosed in a box which can be shut or opened to alter volume too (its not actually as simple as just volume- the closed box damps treble much more than bass).