This is certainly something that concerns me too. In most recipes you can substitute soya flour with ground almonds/almond flour (by volume) but you might need to use a little less liquid. You can also substitute soya flour with the calcium caseinate type of protein powder, but this only works when it makes up a small part of the bakemix (as it tends to give a puddingy result if you use too much).
An up-and-coming potential soya flour substitute is coconut flour. I have done a few experiments with this but it is much more tricky to work with as it soaks up LARGE quantities of liquid. Don't substitute it volume-for-volume as you'll probably get a very dry, dense result.
Re soya bran, this can just simply be omitted, from the recipes in the Low Carb / Low GI Cookbook at least. It's really only there to 'dilute' the carb count and provide more texture. Alternatively, wheat, oat or rice bran could be used (but most low carbers would not want to use such products).
Hope this helps. If you want help substituting in a specific recipe, email me direct and I'll do my best to help.