Pass line level signal through electric guitar
Since you're modifying the guitar then you could do the following:


Replace the mono guitar lead socket with a stereo lead.
Wire pickups output to tip and sleeve as before. The guitar will work as a normal guitar.
Wire your 3.5 mm plug sleeve to 1/4" jack sleeve.
Wire your 3.5 mm plug tip to 1/4" jack ring (middle contact).
Make a stereo 1/4" guitar lead. Balanced microphone cable should be good for this.
Make a splitter box for your amplifier. 1/4" stereo in, 1/4" mono out for guitar amp, whatever connector you like for second amp or second channel on guitar amp.


The advantages with this setup:


Guitar still backwards compatible.
Independent volume and tone possible - sound effects flat - guitar distorted, flanged, etc.