Yeah well that's one reason why I have isolated it through the strategic use of Boss LS-2 Line Selectors.
Here's a schematic for the Pedaltrain 2:

And one for the Pedaltrain Jr that has the front end pedals, EQ, and ISP Decimator G-String:

Here's a photo of the boards linked together with all the various cables in place (except for the cable from the guitar to the wah). As you can see it is pretty neat really for that many cables.
