The MR16 has 16 mono tracks, they have paired 9/10 - 15/16 with the idea that you can "Bounce" your mono tracks 1-8 and record them as a stereo pair OR record a stereo instrument to 9/10 etc. The Fostex logic is for Input A to go to the first track selected with the Rec Select button, Input B to the second track etc.
For the guitar use Input A and (say) Track 1. The Alesis has two outputs (Main Left & Main Right) so you can record a "stereo" signal directly, so connect Main Left to Input B and Main Right to Input C, then select Tracks 9/10 and this will record the Alesis signals directly to a pair of tracks.
When you replay the tracks and mix them, the Alesis will go through unaffected but your guitar can be "located" using the Pan knob for Track 1 between Left and Right (I am not sure what the Focusrite does - I assume that you feed your guitar in and get a mono signal out). This process is called "bounce" and you will record your mixed signal on to 15/16.
For the guitar use Input A and (say) Track 1. The Alesis has two outputs (Main Left & Main Right) so you can record a "stereo" signal directly, so connect Main Left to Input B and Main Right to Input C, then select Tracks 9/10 and this will record the Alesis signals directly to a pair of tracks.
When you replay the tracks and mix them, the Alesis will go through unaffected but your guitar can be "located" using the Pan knob for Track 1 between Left and Right (I am not sure what the Focusrite does - I assume that you feed your guitar in and get a mono signal out). This process is called "bounce" and you will record your mixed signal on to 15/16.