This all depends on the amount of "waffle". The way I would do it normally would be to take the first, 27th, 53rd etc and do a frequential analysis of those to determine the substitution for those, then repeat that for the 2nd, 28th, 54th and so on. However, the "waffle" would throw this analysis off; a little would probably still work because it would only affect the proportions marginally. However lots would seriously mess up the proportions (though it would still be breakable- just harder to get frequency analysis right. The most common would still correspond to "e", but then there's the trouble of working out what's waffle).
If you want a tough code, try this one: