If you wish to still get a refund then I don't think 3 weeks is too long, maybe 3-4 months I would've said to forget about it.
If you want to take the effort, you should get some legal advice from a lawyer to see if you still have a good case. series 2 R33s with an rb20e are pretty rare, so it might be easier to try & find out the average market value of a non turbo series 2 r33 that has the rb25de, this will give you a good indication of how much value to take off because the car has an rb20e.
In my experience, mods such as rims & stereo systems do not add that much value to a car,
the main thing that determines a car's value is usually things like age & condition, kilometres, service history, average market value of the car etc.
As for a loss when you sell, imports such as skylines depreciate in value very rapidly. I bought my series 1 r33 almost 2 years ago for $16,000 & even then I was probably overcharged
(Okay, so my dad financed it for me, but now I make the payments on it )