It sounds like even without knowing much about samurais you have a good idea of what's stock and what's not. It looks to have a home made shackle reversal up front, spring over axle, and your right about the disk breaks not being stock. That truss on the front axle dosnt look great, I would think it would do more harm than good, at least offroad. Value on these things is hard because prices vary so much, with the stock motor I would think $3000 is high but I think that motor swap does add value. The disks in the rear are nice to have and like said above tires ain't cheap.
I would think you can find a ok paint job that would make it "look good" for less $ than the line x. In the meen time could you just use a car cover in the driveway? Anyway it looks like a fun little rig.