Q: Mehtods of aligning the midi(s) (melodic/polyphonics(s,d)/percussive) produced via Melodyne 4 Studio with the original audio?
 
1. Stretching the audio in the X3 Sonar Producer is one method I used to match with the midi(s) durations/lengths; this does not sound professsional. Any other simple methods?
 
2. Is there a simple settings I did not noticed in the Melodyne 4 Studio settings?
 
Note: In Ableton Live 9 Suite, the melody, harmonics, and drums midi (s) are all converted from the audio with the  same lenfths/durations; despite that the algo in extracting the midi is different in these two products.

Sorry no one else has chimed in on your question. I have not done this too much so I am by no means an expert at this but here goes. 
 
If you convert audio to midi using Melodyne and you don't feel that they line up with the original audio then there are a couple of options. you can move the timing of the blobs around in melodyne and then export the midi or once you have midi from Melodyne you could just adjust the midi notes. That seems a much better idea then trying to stretch the audio to match the midi.
 
In my limited experience the midi note on from Melodyne was usually pretty close to the audio but the duration could be off because it has to determine between when the audio event is really off and when it has just decayed to a point where it might as well be turned off.
 
If the Midi data is way off then there might be another issue going on.

Just noticed that if I get my audio inserted into the midi track I got ARA conversion to midi that of the same length/deuration/maybe tempo too of the original audio.  
 
Q: Does this got converted by the Melodyne 4 too?

Yes. That's actually the preferred way. How were you doing it before?

By running Melodyne 4 standalone as well as a Melodyne 4's plug-in for the audio track. Both prouduced midi(s) of different length/duration.

When you say plug in for the audio track, do you mean like in the FX bin or as a region fx (CTRL+M)?
Maybe you accidentally had different algorithms. I don't know, but at least the easiest way works well!

namclow
By running Melodyne 4 standalone as well as a Melodyne 4's plug-in for the audio track. Both prouduced midi(s) of different length/duration.

I think the best way is to drag the audio into a MIDI track. That's the beauty of ARA integration. That has always been very precise for me.

Here is the durations pic for two audio to midi via Melodyne 4 Studio Demo ver:

each of the two audios, the first midi was from ara, the other three were stand alone melodyne 4 studio demo saved for the melodic, polyphonic sustain, and percussive midi s.