I agree. This sounds exactly like post-intake-manifold-repair egine failure. The days, weeks, and months of slow coolant sipping probably ate your bearings. My guess is that you're headed for a new engine, despite babying your car and fixing the intake failure when you became aware of it. Unfortunately we've seen it happen before.
In December I discovered I had intake failure when I noticed the engine overheat. I had the intakes done the next day. Everything'* been fine since then, but I'm still kind of holding my breath, hoping my bearings didn't rust away.
And I'd just like to say it really pisses me off when this happens to good people who otherwise take good care of their car.
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.