Wow, big post, but I've got some time.There are so many variables to what a car's price should be. What I would do is go to KBB.com, (Kelly Blue Book) and look up the suggested selling price of your car. After you get the price you should add about $1000 to that price give or take a little because 240's are getting rare, and are in high demand.
Moving on, if the car has mods it's usually worth less. These mods usually include a body kit, cheap interior work, fart can exhaust, etc.... There are however mods that can increase the value of a 240sx. These include suspension work, (usually coilovers not cut springs) and engine work (turbo and internal work not intake/header).
You gave an example of a guy not touching his car in a year. This could mean a few things:
1- it doesn't run
2- it won't run (1 year is a long time to be sitting)
3- as you said, he's in Iraq
As for parts and your car, you will find a decent running 240 (mostly s13) for 2-3 thousand. It all depends on the condition, mods, and miles. That leave probably around 3K for mods after you do needed maintenance. The first mod I would do would be to upgrade your suspension. You will not regret it. What's the point of going fast if it's only in a straight line. As for suspension I would definately get coilovers. You can pick up some decent ones for about 1K. Next would be engine mods. I would first start out with exhaust. If you're going turbo, don't get a header. As for exhaust, look into BRM. A 2.5'' cat back is good to about 275HP. Any more than that you'll want a 3''. Also you'll want a high flow cat. A full BRM exhaust will cat and resonator will be around 3-4 hundred. It's well worth it. You can find BRM at the top of the 240sx forum.
That leaves you with about $1500. I would start working with the cosmetics of the car. I'm not a big body kit fan so I would put it in the engine. Anyways, I would get some wheels. You can pick up some good used ones or new sportmaxes of Egay for around $500. Depending on the size, tires are going to run you about $130 a piece. That leaves you with not much $ left. I would put it to llittle things like an intake, short shifter, interior crap, etc.... Or you could just save up for your turbo kit. If you want to make say 350HP, your kit is going to run around 3K for a decent custom one.
Well that's about it. About the rear diff, it's plenty strong. Can't you tell by looking at it?!? The driveshaft and diff are huge for a car this small!
Anyways, hope this post helps, and good luck with your build. 
1989 SOHC 240sx Hatch:
Silvia Front, JIC coilovers, custom exhaust
WORK IN PROGRESS
, Nismo 555cc injectors 