You don't need that ancient ffmpeg build; ffmpeg now has a bitstream filter h264_metadata for changing AR and framerate.
Regarding flagging from interlaced to progressive: If your stream is MBAFF and uses only progressive encoding (no interlaced macroblocks) -- e.g. if you use x264's fake-interlaced-option, then it should be possible to change the stream to progressive, but there isn't any tool that I know of that does this. If you are really using interlaced encoding (in particular with PAFF), there is no chance to change the bitstream to make it appear progressive. Your best option is to try to signal at the container level that your content is actually progressive.
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