Adobe Premiere CS5 match sequence settings but change codec
FLV is an Adobe container for streaming video. Historically, FLVs usually contained a variety of codecs (such as FLV1, Sorenson..etc) but nowadays it's usually H.264. Which is to say, the video may already be MP4 compatible. You may not need to recompress the video at all, and could simply transfer it from a FLV container to MP4, bypassing Premiere. ffmpeg is a tool that can do this. Download the 32-bit static build from here and the run the following command:

ffmpeg -i input.flv -c copy -movflags +faststart output.mp4


If the source video is not in fact H264, then try

ffmpeg -i input.flv -c:v libx264 -crf 23 -c:a aac -strict -2 -b:a 128 -movflags +faststart output.mp4