Start with maintenance first spark plugs, wires, cap, rotor, belts, water pump and fluid changes. Alarm, kill switch an most importantly good insurance.
Wheels and suspension would be a good start after all the above.
A tune-up should always be the first thing on your list when buying a new car. You don't know how exactly the car has been maintained in most cases, so it's not a bad idea to do a full tune-up including timing belt and water pump.
After it's tuned up you can start on the real mods. An alarm is really dependent of your area, i'm a few miles from a fairly small town, so I'm really not concerned with my car being stolen. My car was boosted before I even thought of buying an alarm.
its up to you what order to do parts in
i have a low and slow project going on now where it is a stock LS engine with some bolt ons but its dropped and it looks really clean (at least thats what it is going to be like when its done)
or you can make it fast by going straight into boost or doing a N/A build
Either way, i would beef up your security first so your car doesnt get stolen