I like the "unit pricing" method that jps1006 mentioned. At least that way, everyone knows upfront what the cost will be, no room for bickering.
iwire, my situation is close to yours. Owner saw the quote, upwards of $50,000.00, and hit the ceiling. As owner's rep, my mandate is to pick apart the estimate and get the price down (Not my favorite part of my job).

[Linked Image] another reason for contractors to hate engineers [Linked Image]

Bob