I doubt that you need to worry about the OBD I or II issue as long as you swapped over whatever parts were necessary to hook up all the OBD II sensors. You did use the 96 exhaust manifold so that the exhause has two oxygen sensors didn't you?
I does sound like you still have a few issues to work out to get the shift linkage to work properly. The mounts may have something to do with that.
The fuel pressure readings do indicate that you don't have enough fuel reaching the injectors. Before condeming the pump you should check/replace the fuel filter.
