Would you consider putting the 3rd paycheck in a month straight into savings (counting it in your annual figures but not in any month).
If the bad spending months are due to discretionary spending, I'd keep them in to give myself a face punch. If they are due to lump sum payments for annual expenses, (annual insurances, that month when you have a load of birthday presents to buy, membership fees), you could account for them on a monthly basis (either putting money away into a sinking fund, or just splitting the cost across the year).
Or have a category for 'one offs' and include that in your annual figures but not monthly figures (both annual payments and extra paychecks).
I would think about what outputs you are looking for (saving rate, annual expenses, etc) and calculate each in the most appropriate way. If you are working out monthly expenses to calculate your 4% number, you need to have all your annual spending in there somewhere, excluding genuine one offs (your own wedding?) but including a provision for home maintenance and annual fees. If you are working out monthly expenses to see if you had a good or bad month, it makes more sense to annualise the lumpy but necessary spending.