Re setting stops; I am not a keyboard player, so I play GO with midi files generated by notation software; I've so far only used GO2, and Finalé Songwriter to generate the Midi file. Initially I found trying to select stops was a right pain in the wotsit I tried using an extra staff on a separate channel and using tied chords to generate note on/off, it worked but was awkward to say the least. I then started using Midiocre to edit in Programme change commands (Cx) to set divisionals having manually set up the divisionals and saved in memory for the work to be played. This works very well for me, but is not much use to anybody playing a keyboard. Changing instruments on a keyboard will achieve the same result, however the only keyboard I have requires 4 key presses to generate i Cx command (function select followed by 3 digits on a numeric pad) so wouldn't be much use except at the start of a work or movement.
In Songwriter (notation software) I set each staff to a separate midi channel and each midi channel plays one keyboard or pedals. I'm using an extended Stiehr-Mockers organ, with Swell set to channel 1, Great to channel 2 and peds to channel 3.
Assuming 8 divisionals per manual select them using Cx 00 through 07 on the channel associated with the relevant manual/pedal, the registration for the start of the work can be assigned by selecting the appropriate "instrument" for each staff to select the required divisionals.
For subsequent settings I edit the midi file using Midiocre inserting a Cx command at the point in the midi file where the registration changes. It as actually possible to change registration more than once in a bar/measure. For a keyboard player select an instrument that generates the CX command number for the required divisional.
The limitation with the basic GO screen is 8 divisionals per manual, however this can be extended in the .organ file, to test this I have 10 working on each manual.
Midiocre is available here --
http://download.cnet.com/Midiocre/3000-2170_4-10019301.html
Open your midi file, select the track to edit, then select "Events" right click an entry to get a drop down of options, "New" /Midi opens a further window to add or alter any valid midi message like programme or control changes, note on/off and also to set the position within a measure when the change will take place.
Hope this will be of some help, not sure if there are any changes in GO3 to affect registration by this method.