First question: To send a certain signal, you should send a number of durations that are "close" to the one the receiver expects. It will be recognized if (and only if) it differs from the expected one "just a little". If you send a "dirty" signal (i.e. one that deviates from the perfect one, for example since it is a physical measurement), it will often work "most of the time", but not as reliable as with a perfect one. For example, it amount of allowable disturbances that can be tolerated without breaking the recognition is less. So "cleaning" your signal is desirable, however strictly speaking not always a necessity.
Best tool for cleaning signals is IrScrutinizer. It identifies the signal (assuming that the "dirtyness" is not too large), and then replaces it with the ideal, computed signal.
I would strongly recommend taking some time to "play around" with IrScrutinizer.
Second question: There are two different "forms" of IR signals in your message; first and second consists of the durations expressed in micro seconds, the even ones (first, third, fifth, ...) being on-periods ("flashes", "marks",...) , the other ones being off-periods ("gaps", "spaces", "pauses",...). The third one is however a true Pronto hex, my description
[Link: harctoolbox.org] contain just what you need to know (or actually a bit more than you need to know right now). Note that all numbers are four digit hexadecimals, with no comma in between.