Hmm.... tough one, and something I have only ever tried a couple of times. If it needs that, usually I start again :-/. I have never used X3, I stopped at X2. That being said, IF I was to start, do bass drum, create a tempo map from that, then snare, then align the rest to those. quantatizing audio files of drums though, yuck. I know guys who do replacement drum stuff and all that. Good luck, hopefully someone will chime in that actually has done more than me, not hard :D.

I do a lot of this stuff through various methods via a combination of Samplitude, Melodyne pitch to midi and manual labour, not to mention, even repairing or spectral cleaning out some notes prior to replacement. I'm all for replacement but, (if you refer back to my post on headphone bleed) headphone, or just bleed itself becomes your greatest enemy. Its a Pandora phase box.
Mono comparisons, using normalization to clinical zoom in on the softest transients or bits, then undo is part of the process. I will even use this to kill bleed

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In a nut shell, I will usually delete as many unnecessary tracks, fix and line up all the keepers, remove the bleed creating phase problems, parallel blend replacements and use an emulation reverb to help glue it all back together so it sounds more like it was tracked in a nice room. Works really well but its a task.

I finally found what I was doing wrong. I needed to use the option Merge and Lock Markers :)
I'll make some tests, we'll see !