That sux!
I dont think they wanted to scare you with the real labor estimate....parts are always the cheapest......what kills is the labor...which is usually triple to quadruple the cost of the actual parts. So $1000 labor for $4500 in parts is way too low.
Best bet would be would be to just go out and get a wrecked or non-running donor car for $1000 and transfer everything over yourself.