Here is my 2 cents... Don't assume you got screwed, some of which might just be miscommunication. If I were you, I would start by calling the parts department (not service) and just generically (as a John Doe customer) ask about the ECU (for some reason I am thinking the parts you mentioned are just a "superseded" part). I believe keys can be recoded, but as far as giving you a new key free, I don't see that happening (they are relatively expensive), but they should have presents the option of purchase.
Regarding what you said about "questionable parts and things that are wrong", if you elaborate more, you might be able to get some additional feedback from this forum.
Finally, regarding servos, 18 years does produce wear...are you saying that they actually caused the damage? If the driver side "flooded", what was source? Is it possible there was water in door that caused lock problem?
Best of luck, and I feel your pain man...just remember s*** happens, and some poops cost more than others.
