i remember helping secret52(worklog--though his was a Code 3 Compact) with installing some of his siren parts, though he never integrated it into the touch screen..
it should be entirely feasible with a fusion brain, though i don't have one, and never programmed one, so can't help in that aspect.
what do you mean by stereo controls?
rca-connectors are over rated.. it is a safe bet that any adapter above $2-3 is good enough to not adversely affect the sound quality (unless you are really into sound quality, and can tell the audible difference between polypropylene, and electrolytic capacitor crossover components) i would not say that you need to worry about a sound card unless you have more complex car-audio needs.
gps shouldn't be an issue, but i don't use it, so can't help(the bu353 is a popular reciever)
cost: i would expect to be around $500-1,500 obviously depending on parts cost(the monitors are a more expensive part), my first setup was about $800 w/ all brand new parts, but has now risen to over the $1,500 mark after going through 3 sound cards, and a different motherboard..
netbooks seem to be getting more common around here--the atom processors are good for most tasks as long as you don't expect them to be super snappy. custom built systems depend on the quality of the parts, but in most cases, should be just as good, and imo, easier to service because you built it, so you know how to fix it easier..
i don't know how much your techie-guru knows, but most of the IT-Admins i talk to about my carpc aren't too crazy about the idea..