I am the guy with the 98 SE that exploded a couple of weeks ago. I have another thread going as I try to get the car running again.
Yes, I thought of all those things. I replaced the FPR, even though it tested OK and had already been replaced on the recall. I checked the compression and it is reasonably good, so the valves seem to be closing at the correct time. When I had the intake manifold off everything looked OK, but you can only see the push rods and the intake valves. I didn't get any codes so I don't have any other clues yet. As soon as I get it running, I will post back to let you know how it runs.
By the way, I call it an explosion, but really it was a bad backfire that broke the plastic UIM and dislodged the fuel rail. This caused the fire.