Hmm, I feel dumb, but I don't get it. I don't see why you have to do this. But even if you must, I am not sure you should.
If you do it my way, it is very easy to understand and saves on processing cycles. I think right now the mutation routine scans through every line of DNA code and decides whether it wants to mutate that. This requires all those random numbers to be generated and some calculations. But if you do it my way, then the routine would do a quick single check on how many mutations should offspring get - and you can get that from the "1 in 36" frequency using Poisson distribution. If the number is 0, then the whole DNA is copied in one step, no need to run the mutation routine at all. If the answer is 1, then it checks which mutation this will be and applies it to the DNA. If it is two, then it runs the routine twice. At any realistic mutation frequncy the probability of getting three mutations in the same offspring should be so low, that it can be ignored completely.