Chem, if you were going to replace the entire hydraulic system, it would be very expensive (around $1200-$1500, my guess). Outside of a severely damaged/scarred rod, I would think you could not have to replace the entire system. All I did was replace the endcaps/seals and then bleed the system to get rid of the bubbles.
If you're looking to install a system, you may want to check online for a used system. Might find one cheaper, perhaps even one that you can just rebuild, bleed, and get back to new. Not sure how much cheaper they'll go, though.