I just want to say that I disagree with how you're going about dealing with the shop that has your car. See, you're empowered now. You have real information about what happened to your car. They even said you have a hole in your intake. All the other things you say they said, like "thin valves" and "worn rocker arms" and "bent rods" and "fuel injectors sticking open" are just BS. I mean really, "thin valves" ??
But now that you're empowered with real information about what went wrong and what it normally takes to fix it, you want to "go in with guns blazing and stick it to them" (not actually sure what that means, but I hope you don't mean it literally) -and yet you *STILL* say you want them to fix it for the [originally] quoted price.
Look, you already know you're dealing with a shop that would rather tell you your entire engine is toast because of a hole in an intake manifold. They already quoted you a course of repair that, yeah, will get your car running again, but for that price you really can go out and buy a 1998 SE in perfect running order.
At this point it may very well be cheaper to buy another Series 2 3800 engine and have another shop drop it in. You should be researching other shops, and tow your car out of the one that has it. Get a used engine and swap it in, if it isn't feasible to just reassemble your existing engine with a new upper and lower intake manifold.
97 SE, teflon wiper blades, Dunlop Sport A-2 tires, Leather steering wheel cover, Pioneer DEH-P480MP mp3 CDRW head unit, Pioneer 12-disc changer, iPod hookup, Boston Acoustic 3 way 6x9'*, Boston acoustic separates in door pods, Alpine 4 channel amp in trunk. Magnaflow dual outlet muffler and Ractive stainless tips. Autozone rice pipe and K&N 4750 intake kit. Clear corner lights. Energy Suspension end links.