Sorry to spoil your party, but lines of code is one of the worst metrics possible, especially if people know their assessment or bonus is in any way tied to the metric. It actively encourages cut and paste programming and other attrocities. It's more effort, but why don't you categorise the workload in terms of expected effort for one person, based on your historical data? Or, get some programmers to agree to do a few projects redundantly, rotating between pair-programming and individual, so you can see how the same programmers go at each. As one good programmer can be more productive than two average programmers (I vaguely remember an old IBM study concluding someone in the top percentile was 27x more productive than median), it's useful to see the same programmers doing it both ways. If objectively discovering the right process through such an experiment is too costly in terms of lost short-term productivity, then you're better off not bothering with the LOC metrics anyway... good programmers knowing their work arrangements are being based on such will probably be highly unimpressed.
Remember that there are also intangibles involved... pair programming - IMHO - forces people to keep focused, and to make design decisions that are more rounded and professional. Just the social contact can help relieve boredom, though it may stress some people too. My suspicion is that - whether or not it's faster to begin with - it makes for better, more maintainable results. It also ensures skill and knowledge transfer. You should factor in such intangible aspects as best you can - maybe doing interviews or anonymous surveys with the trial participants.