The basic Factory Setup is described on the wiki. To see what's in each instrument slot for the sampler or audio unit slots, you should launch the EigenBrowser, then bring up the instrument controls (main mode key, and right col, key 4 - looking down from the breathpipe) as per page 2 of the Pico Quick ref. The select the instrument by holding the mode key (right col, key 1) and pressing the key corresponding to the instrument in the left col (as per section 4, pg 4 of the Pico quick ref). Then hit the third key down on the left column. This is described in the tutorials (Pico tutorial 3).
Getting a violin sound in slot 5, would require you to have an audio unit capable of producing a violin sound. Alternatively, you could reconfigure the cello to sound more like a violin. This requires a suitable impulse-response file, and some modifications to the cello oscillator. Geert describes how to do this in a recent Eigenharp clubhouse recording on youtube (#33 I think?). See also the wiki page for the Cello Oscillator.
Replicating the cello in slot 5, would require some rewiring in Workbench, which requires a little more familiarity with the EigenD internals ;-) Perhaps a bit adventurous for a supern00b for the time being?
I'm not sure if you can change the reference pitch. You can detune the samplers, and other oscillators individually using the Stage interface (and obviously via belcanto), but I don't think there's a single place to change all of them, nor do I think this impacts the Audio Unit agents?
D