Vocoder sounds are a ****. Don't know anything about the vocoder pedal you are using. I use the mvocoder from melda occasionally and yeah, it isn't really easy getting clarity. The vocal you are working from must be loud and articulate with much care to ennunciation. Parts of spoken and sung words are typically not so loud and don't carry over well so you must exagerate a bit to get a good envelope. The dynamics of the carrier tone are very important as well - you need a strong, steady tone because if you are putting the vocal envelope on a weak sound it won't come across - so in your case the guitar should be full and steady so you have a solid tone to shape.
Blending in some of the original vocal is very helpful for clarity.
Are you wanting to pull this off live? Because if not, a guitar pedal vocoder probably isn't the best way to accomplish the vocoding on a recording(ps those shoes is an old favorite of mine btw). I'm betting the original was done with a talk box, as Mr. Walsh was a fan.