If the .pdf user manual for the Firestudio 26/26 on the Presonus website were not corrupted, I would be able to answer this relevant question: are you sure you can configure the Firestudio to route its pre-amp outputs to the ADAT lightpipe? If that's possible, have you done so?

My guess is that the routing defaults to the Firestudio ADAT outputs to be connected to the FireWire output from the computer. When you run a lightpipe from this output to the Digi ADAT input, PTLE will see something connected, but it has no way of knowing anything about the internal Firestudio routing.

As for clocking, you can indeed make the Firestudio a slave to the 003, but you would need to have an incoming digital connection to make this work: either a lightpipe connected from the 003 ADAT output to the Firestudio ADAT input, or an S/PDIF coax in the same direction. However, I would suggest clocking the 003 from the incoming ADAT from the Firestudio.

I have routed the signal to the ADAT out by using the CPL software and have also clocked the 003 from the Firestudio, but PTLE is still getting no signal. Could have something to do I/O settings under the setup menu? If so, how can I set it up?

Usually both products include various connection setups in their manuals. What do they say in regards to your particular setup?

You'll definitely have to set up the routing in ProTools if you haven't already.

Both manuals confirm that my setup is possible. The Firestudio is able to route its preamp signals to the ADAT out by using the CPL software. The Pro Tools manual declares that it is capable of recieving signal from an outboard device, as long as it is ran through the 003 first.

In order to set up the routing in Pro Tools, I think I must go to Setup>I/O>Input tab, but after that I'm not entirely sure what to do. Its graph shows eight optical ADAT input slots. Is there some way to activate it or something?