Alex Dinn, I will attempt to answer these questions:

Must I use only 44.1 Khz Ir?

Yes, because that is the (highest) sampling rate of the EPSi

Do you use Mono or stereo IR?

Use stereo if you have use stereo effects. I have a stereo setup (stereo power amp and 2 FRFR speakers) so I just go with stereo . If you have a mono set up you will not hear the difference of a stereo ir/effect combo.

Why do you set the intput on 9 and the output on 3?

Those are the recommended settings from Singtall who has the most experience with the 11 rack/EPSi, you can change these if you want to suit your setup, aim is to avoid clipping/distortion of the signal.

What are your fav IR from the ownhammer modern pack? There are so many...

I hear you brother , I am still working my way through the vintage pack. It is a difficult if not impossible question. as the answer depends on the tone you are after! This is why some bands spend years in the studio trying amp/cab/mic combos for that perfect tone!