I keep opening this thread and wanting to post my methods/experiences but it will be a loooooooong post because it's all quite complex and I actually DID switch to another DAW to get through my recent alignment work (entire live session of 8 song both recorded twice without a metronome). I didn't really want to blather on AGAIN about another DAW.
BUT, since you asked... I switched to Reaper just to get all the takes bulk aligned and now have imported the resulting files back into Sonar. Since the Reaper demo is fully functioning you can go this route without dropping a cent (but of course it's technically a $70 purchase for home users).
Basically what I did was set up a Reaper project for each song on the "album" and imported the two takes for each song as their own set of tracks (so tracks 1-9 were take 1 and tracks 10-18 were take 2). I then grouped the clips (or as Reaper calls them... "Items") of each set of tracks with each other (so all the clips of Take 1 grouped together, all clips of Take 2 together).
In Project Settings I changed the timebase setting from "Beats" to "Time" (this makes it so the clips don't stretch when making Tempo changes which WILL be done later but not yet). With this setting I created a Tempo map of the first set of Tracks by inserting Tempo Markers on the dowbeat of each measure (and I added more intricate Markers as necessary for things like odd fills/time changes as well as inserting Time Sig changes as needed).
Once everything was mapped I created Splits across the first set of tracks at the spots where I have put Tempo Markers. Bbefore doing this I adjusted the Auto X-Fade On Split settings... or whatever it's called to create an extremely short linear x-fade for each split... like under 10ms. Since the splits/x-fades were joining the same original clips having it short seemed like a better idea to make them less intrusive to the original sound (I was just guessing that was the right thing to do though).
Then I went back into Project Settings and switched the Timebase thingie back to "Beats" to allow stretching upon Tempo Changes.
All I have to do at that point was double click on the Tempo Markers and insert the tempo I wanted for each measure/section and the clips automatically stretched to accomodate while remaining locked to the timeline (this alters the tempo map of course).
Since this material has a lot of speed ups/slow downs/drastic tempo changes I spent a good amount of time fiddling with the tempos until it all sound JUST right and everything flowed how I wanted. I did a save as of this version to preserve the splits for further editing later if need be.
THEN I selected all the clips and used the "Glue Items" option (Reaper's version of Bounce to Clips) which created full clips for each track with the tempo changes applied. BTW at NO point did I get any artifacts or unwanted noise before (or after) gluing even with drastic changes/stretches.
Once that was done I moved on to the second set of tracks. For that set all I did was go through and created splits at all the downbeats and essentially everywhere else I had inserted Tempo Markers on the first set of tracks. I used the Slip Stretching option to line up the splits on the second set of tracks with the first set of tracks (Slip Stretch is Alt + Shift IIRC). Since the clips were grouped all the stretching applied to all the clips (as opposed to Sonar which for some extremely annoying reason ignores Selection Groups when Slip Stretching).
After that's done I glued the second set of stretched clips.
Bingo bango I now have two full sets of tracks sync'd to each other that I can edit/comp together in Sonar or whatever program I want.
The plan now is to comp together the best bed tracks (drums and vox actually because I'm retracking everything else but don't have access to that drummer or the vocalists anymore). Once I get those comped super takes together THEN I'll start aligning any individual hits or sections that still need work. I'm hoping to use the Audiosnap Merge and Lock function for this but if it screws up I'll just head right back over to Reaper and use it's finite transient/section editing tools.
Please note that although I did research all this quite a bit it was really my first major undertaking in Reaper and some of the things I did may not have been necessary and/or I did some things the long/hard way. Example... I''m not quite sure I needed to create the splits on the first set of takes and I may have been able to do the stretching on the second without the splits (by using the transient stretching thingie). Also I'd like to figure out a way to apply the same tempo to multiple tempo markers (like if there is a long stretch with a steady tempo) as opposed to entering the same tempo over and over again manually (deleting Tempo Markers and letting one marker control an entire section works but then those markers are gone so they cannot be tweaked/changed again and the reference points are lost for the Slip Stretch alignment of the second set of tracks).
Anyhoo... still a very truncated version of what I did and I actually want to create a vid of this procedure when I have time but might help you figure things out for now. It's a looooong process (I can plow through one complicated song with two takes in about a day after TONS of practice) but it works brilliantly. Everything stays in phase and the sound quality is great. No glitches, crashes or corruption at ALL.
Oh... also in Project Settings I switched the Render settings to the highest quality as well. Reaper's default is middling quality.
Sonar is my baby fo' sho' but I'm really digging having Reaper as a secondary DAW for things like this where Sonar just kind of chokes on itself.
REALLY hoping that some better time stretching tools come along in Sonar which is part of the reason I was hell bent on getting the Lifetime Upgrade. I'm sure they'll get to it someday. Just not today.
Sorry for going on about another DAW. Poor form but sometimes you just need to get things done and I see nothing wrong with using tools that work to get on with things in the warm loving embrace of Sonar. ;-)
Cheers!