Sounds like what you're describing might be caused by not having the guitar signal loud enough when it goes into the computer. I see that the Alesis IO26 can amplify mic-level signals. Are you plugging into a line input? Is there a trim adjustment on the line input to make it work for the lower-level guitar signal? If not, you might want to try running into a mic input instead.
Alternatively, if your guitar amp has an effects loop, you might try
running the effects send out into the computer instead of the guitar, and the computer's output into the effects return.
I am using the AudioFire 4, which has two channels with preamps, so I'm plugging my guitar into those. It works well because I can run my Copeland hex pickup signals into those 2 inputs, and then process them separately in Guitar Rig using the Split modules. Very cool.