The P28 wasn't a Prelude ECU, the P13 was. Because of the lack of software support for the P13 (it's kind of a bastard stepchild in the Honda ECU family) and the fact that you don't already have an ECU for that engine, I'd go with a P28. It's going to have to get tuned for that engine anyway, and most of the tuning programs can start with the H22 or whatever maps using the P28. All Honda tuning software supports the P28, not all really support the P13 that I know of. I'll spare you the boring reasons why, they're not important.

If you have a 94 Accord, any OBD1 (92-95) Honda ECU should be a drop-in without any problems. Now the engine side of things, that may be a different story. That I can't say, because I've never touched that engine before and I'm not much of an Accord guy either.