After playing with 555s I don't recommend them at all, but to answer your earlier question about how to deal with the audio path, you would use the 555 as an LFO to drive the LED side of your vactrol. Two problems with this approach:
1) As mentioned before, the 555 would drive the vactrol, but you might have a hard time trying to get the signal going through the LDR side of the vactol to be the same volume as the bypassed signal when you press the momentary foot switch.
2) To fix #1, you could use a little preamp circuit to adjust the stutter volume, but now you'd be sharing a ground with the 555 and it's VERY difficult eliminate the popping of the 555.
My recommendation is to get in touch with Jon Patton (Midwayfair) and ask him which LFO he'd recommend. He has at least one simple LFO that doesn't use a 555. You could just use the rate pot and use fixed resistors for the depth and wet/dry controls. As for the footswitch, just use a momentary switch instead of a latching one, and wire it the same as you would any other bypass switch.
I just thought of an option to deal with the volume difference between on and bypass states. Intead of using a bypass switch, use a momentary DPDT on the LED side of the vactrol to select between the LFO output and an uninterrupted voltage from your power supply. The guitar signal would always be routed through the LDR. The LED would either stutter when the LFO is powering it, or it would be lit constantly when the switch selects straight power. This option allows you to have two separate grounds and would probably eliminate the popping issue. You might still want to use a CMOS 555 to suppress the noise even further.
The downside of this option is that having your guitar signal always going through the LDR might negatively impact your tone. Also, you might still have popping problems if other pedals are fed from the same power supply as this pedal.
If you get this going, you'd do us all a huge favor if you would name it the Burst Box. The Burst Box is a mythical effect that at least one person believes exists, sort of like the Yeti. It would be good to have a real pedal with this name. See this thread for a laugh when you have some time:
http://www.diystompboxes.com/smfforum/index.php?topic=76932.0