You'll probably need to pull the fuel pump and make sure that something didn't get messed up then. I've never the pulled the fuel pump on a 3rd gen, but I've replaced them on several other types of cars. And on some of them, the fuel pickup extended below the pump. If the pickup falls off or splits, it won't pick up fuel when it gets below a certain level. It's worth looking at. In case you don't know, you access the fuel pump from behind the rear seat. There are two access panels in the hump behind the rear seat. Pull up the carpet and you'll see them. The fuel pump is on the driver's side. Here is a link to an online service manual...
Honda Shop Manuals - 1988 Prelude
Sorry I can't think of anything else at the moment.