Bruce,
I wrote a PC application 6-7 years ago that scanned IR & RF codes (recorded using a soundcard), identified them by manufacturer's type, and allowed converting them to Pronto and other formats.
A couple of tips: Accuracy is not critical as most remotes, being battery powered, allow a fairly wide range on pulse/space durations. 20% will work with most.
And, as you noted, most codes have a lengthy space between copies and/or have an initial pulse that is significantly wider than subsequent pulses. You can look for these to determine the end(s) of a code rather than having to predefine the number of bits.
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