I don't have an Eclipse, or a PCM92, but I do have experience with MIDI, etc., that may be of assistance.
First, the BNC Clock Out has absolutely nothing to do with MIDI Tempo… it's used to sync the sample rates of the digital converters.
Secondly, if you have your Eclipse set up as suggested by IDeangelis, run a MIDI cale from the Eclipse MIDI Out >> PCM92 MIDI In. Run a second MIDI cable fromthe PCM92 MIDI Thru to the TimeFactor MID In.
Third, in the PitchFactor, set the MIDI program change receive and MIDI clock receive options to ON, also as suggested by IDeangelis, see the PitchFactor's UM for details.
Last, since you said in your second post, you've already got the PCM92 to respond to the MIDI clock sent from the Eclipse, but if not, refer to the PCM92's UM for details.
Mostly, this sounds like a cabling issue. Your system should be connected as follows:
Eclipse MIDI Out >> PCM92 MIDI In
PCM92 MIDI Out >> PitchFactor MIDI In
Note: I'm sure you already know this, but the above has nothing to do with the audio path, so you'll still need to connect everything with audio cables, too.
