In my hands, recombination effeciency remains very low without Red proteins in E. coli. The main problem is going to be selecting against nonspecific transformants who have uptaken the linear DNA without inserting it into the genome in your preferred orientation. It is possible for the bacteria to use the DNA as a plasmid, which is why you'll need negative selection after transformation. If your electroporations are around 10^7 to 10^8 then you can expect 1-10 recombineered colonies in E. coli using red proteins to bring in a 3kb construct. Point mutations may work better, but it sounds like you'll be needing a larger integration.
Also, I dont think this experiment would be able to get enough photons out of bioluminescent yogurt. When is it supposed to fluoresce?
-Sean
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