this might be better moved to the newb section as much of it deals more with the general carpc, and not the audio install.
i will try to help with what i know, but don't use am/fm or obd..
it sounds like what your trying to do is perfectly feasible.
the hdd is really personal preferance. if the hdd's are mounted decently-- preferable in a area away from the subs, either version will work. ssd's are def. much more desireable, but to many the extra cost is not a justifiable expense.
it seems like you are more spl-based then sq-based, so i doubt it, but have you considered having the carpc manipulate the audio?