Is there a way to control the stops, couplers, pistons,expression pedals from the Rodgers console, via the midi interface.

Unfortunately, I'm not familiar with the Rodgers organ console.
If it has additional controls besides the keyboard that also send MIDI signals, then you can certainly use them.

You can see whether commands are being sent, and which ones specifically, in the Organteq MIDI monitor (found in the MIDI Mappings / Action mappings window).

So, if the console has usable controls (switches, knobs ...), you can assign them to your desired Organteq controls using the MIDI Learn function.
Alternatively, you can also do this manually in the Action Mappings window.

The Organteq manual describes the procedure in detail. It's definitely worth taking a look at it.
Look at C:\Program Files\Modartt\Organteq 2\Documentation

Hello all, I am just setting up so that I can play through the  software to the Rodgers digital 2 manual organ. No problem with the midi interface. On the software, how do you separate the manuals?  at the moment everything plays on everything (including
Pedals on the manuals). I’m sure I’m missing something elementary, yet essential! Thanks for any help you may have!

Hi,
if the two manuals and the pedal of your organ console send on different MIDI channels, which I assume they do, then assigning them to the manuals and pedal in Organteq is very simple.

Open the MIDI Mappings window and select the Keyboard mapping tab. Here you can choose a suitable mapping preset as a starting point and adjust it to your specific needs if necessary.