Edit: Before attempting ANY of this make sure you do a "Save As" of your project so you don't lose your original project as you play around. Also I usually make copies of any clips or tracks I intend to do things like stretching on so the originals remain available so I can try again without using "undo" and or I can try out different techniques and compare the results (and choose the best ones). You probably know this but I'd hate to lead you to a crash or have your raw waves get screwed up because I urged you to get all fancy arse.
Original Post...
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Oh... yeah, you should not be bouncing all the tracks together before doing the stretch (ideally). Stretch your individual mono tracks individually (you could stretch them all at once if your computer can handle it but either way... leave them as separate tracks when stretching). Then "bounce/render" the stretch to each individual track on at a time (still separately).
That should work better. A lot of stretching stuff relies on the transients in an audio clip so by bouncing/mixing all your clips together you likely made things harder for the stretching stuff to really detect the transients for the stretching (like the multiple clips created less precise "splits" at the transients so it futzed up).
As automatic as this stuff is these days it is still a rather precise procedure that requires your splits be at the best spots on the clip (at the transients) to work well. So if you do them separately it should work better BUT if not see if there is something called a "Loop Constructor" view which allows you to get right into the wave and adjust where the splits occur (like sometimes the transient detection will miss some transients in which case you add them or it detects the transients too early or late in which case you move the splits to where the actual tranients occur).
That is more "GrooveClip Looping" stuff (as opposed to the Izotope stretching done in Track View) but it can acheive the same thing.
Again it depends on what features that old version has but if you got this far I can only assume that you have the tools you need to make it happen and doing whatever stretching you did here on the INDIVIDUAL tracks and then bouncing the INDIVIDUAL tracks one at a time you'll get less artifacts.
Look into the different "offline algorithms" you have access to as well.
Sorry to be vague but as I said... I'm an X series brat so I can only guess as to what you have access to. Check the manual for some of the terms and techniques I've mentioned here.
Also know that the more drastic the tempo change the more problematic it becomes. So if you are doing something nutty like going from 100bpm to 150bpm or 200bpm the results will be less desirable and/or you will REALLY need to get in and place your splits accurately by hand in the Loop Constructor (if you have it).
If you are only increasing/decreasing the tempo by say 5bpm's then it's usually going to work out better/easier.
Also disable ANY and all effects before bouncing (or disable them from the bounce if possible) because transient detection works best on clean, dry, articulated tracks and let's the software work better. You can add the effects back in after you have bounced.
Certain dynamic effects though may actually HELP define the transients better such as compressors or limiters that even out the peaks a little but if you totally squash it (so the lower parts are closer to the peaks and make the transients less defined) then it starts to not work so good.
Basically heavy distortion or tons of reverb is back for transient detection. Something like a limiter that accents the transients a little better MAY help... but due to the bounce you may be stuck with it.
Ideally you want a nice, clean and cleanly played part with defined transients (in the case of guitar cleanly picked notes and chords).
Hopefully this points you in the right direction. It's a bit of a confusing topic but I have been VERY impressed at some of the results I've gotten with Sonar using some of these principles.
Cheers.