You are making it very hard for yourself by attempting to align your project to the original audio. Forget that. What you have to do is start by creating a midi session that follows the song correctly and starts at the initial tempo of the original tune.
 
Someone is going to have to figure out the tune completely, chords and all time sig changes if they are there. There is no getting around it. The best way is to still transcribe the original audio onto a chart. That is the time to work with the original audio BTW. While you are figuring it out. DAW's make it easy to stop start and do sections at a time slowly. Don't worry about aligning the click to the audio.
 
Now you turn off the audio and construct a basic midi session that matches the songs arrangement perfectly.
 
Figure out the start tempo
 
Construct a click track (1/4 notes) and create all the time sig changes that match the song. You have just transcribed the whole arrangement onto a chart. You use that to quickly program up your session.
 
The idea is to create a basic arrangement/session in midi.  What I do is put in a basic piano part that simply plays out the chord progression and a very simple bass line. I start with three things. A click that agrees with the music arrangement, a basic piano chord and bass track. Have at least two bars preceding.
 
For session musicians you can turn all the above into audio and give that to them along with the tempo info. They can align their DAW to the same tempo if they want but they don't even have to do that.
 
Next work with a guitarist/session players who can play out the entire arrangement and correctly. You need the chart at this point to give to the guitarist. You tell them there is two bars leading in. If they are good enough they will sight read the chart and play the arrangement perfectly. Even if they need to get it right in sections they can, but they must only submit a total wave the whole length of the music back to you.
 
You should be able to align the start of the session recording in your arrangement and it should match your audio track right to the end. At worst you may have to cut in a few areas here and there and realign manually.
 
The original music may have some (more obvious) tempo variations on purpose as well as the time sig changes. You will need to identify those areas if you think they are important enough and if you feel they are, then you will have to program your original midi track to do something similar. And do all that before creating the first audio track for session players to play against. Otherwise leave it at a constant tempo. Live session players tend to play nicely around it anyway giving the track some timing feel.
 
Towards the end of your tracking work you drop out the original guide midi bass and piano. By then those parts may be replaced by live players or you sequence much better parts there. Drums may be a VST or a live player in the final mix as well.
 
This is how I have always done it for either original music or covers. Sometimes all the parts end up live, other times part midi and part live etc..I usually turn any midi into audio just prior to mixing.

robert_e_bone
I can click on the time formats displayed to toggle through the various formats, but where do I type in a SMPTE value?
 
Bob Bone
 

THE FOLLOWING IS INCORRECT. DISREGARD. Sorry.
 
Sorry. Had to put my laundry in. You should be able to double click on the numbers and then you'll be able to type.

Double-clicking does NOT allow data entry in the transport Now Time, or in the smaller one above the tracks in the track pane.  Any clicking, single or double, scrolls through the various format displays.
 
To Jeff, thank you for the incredible amount of time and detail in your post.  That is the conclusion I have come to.  I did come to the conclusion that I can bounce all of the scratch clips the guitar player created into a single track, and then I won't have to worry about lining things up - it will simply line up to zero.
 
Oh, that mythical 'someone' you referred to is unfortunately me.  I will have to chart the original tune completely, to lay the meter base as the foundation for the rest of the tracking to take place properly.
 
That way, I can then get all of the time signature changes mapped out and inserted into the project.  Then I will delete the scratch track and have the guitar player re-track in final form.  I will also then be able to add in all of the various midi tracks needed (bass, drums, violin, keys), and that should do it.
 
I DO wish Sonar had a little more depth to these time formats.  That would allow SO much greater precision and ease of doing things like I am wanting to do.
 
So, it seems as though I will be able to get through it with the bounce of the scratch track and the re-tracking.
 
Bob Bone
 

What? Okay, I'm gonna have to fire up the DAW. I could have sworn you could type data into those fields. Sorry, man.

Wow. You're right. Where the heck did I get that idea from? X1? Maybe I'm thinking of Nuendo. Anyway it's pretty silly that we CAN'T do that. Both right and left click change the format. They could at least make it so right click allows data entry.
 
Anyway, Bob try the Clip Inspector route. Paste the clips close to where you want them then select the one you want to position (this will only work one at a time if the clips are going in different places), open the Inspector (I), select the Clips tab. Under the Properties sub menu there are three fields named Time Format, Start and Length. Click the Time Format and a dropdown menu appears. Unfortunately the only options there are M:B:T, Samples, H:M:S:F and seconds so if none of those work for you well... I guess it won't work. This time format is independent of the project format so you can have your project display and ruler set to M:B:T and the clip format set to Samples and whatever you type into the Start field will be where the clip starts. So just select the time format you want and type in where you want it.
 
I hope that works for you but I'm probably still missing something. Sorry about the module confusion. I swear I used to be able to do that. The fact we can't is just silly.
 
Cheers.

Thanks - for some reason I thought we could do the double-click thing too, but no dice.
 
Yes, it is silly.  They have the ability to deal with things already, in terms of converting from one format to another.  It doesn't seem like much of a technical stretch to be able to actually USE those multiple formats for doing precisely the kind of thing I am trying to do.
 
It seems though that I can do the bounce to a single track, for all of the clips the guitar player created, and that will eliminate the need for doing any lining up, as it will simply align with the beginning of the project.
 
I do think I will give the Clip Inspector tip a try, and I will post back on it.
 
As a keyboard player (mostly - I do some guitar though) most of what I do is in the world of midi, so I still have a great deal to learn about using Sonar.  I have developed some measure of theoretical know how for audio tweaking, but have a long way to go in terms of applying that knowledge.  
 
One of the great things about this forum is the collective skill set that exists, with enough folks who know particular areas really well make it possible for others to learn how to bolster things needed to make it all work.  It's pretty cool, and I am constantly learning from the threads here (expect for the grumblings and spam posts).
 
Thanks to ALL for the assistance, 
 
Bob Bone
 

Oh, I did have success in specifying a MBT value close to where I wanted to paste a clip, then used the +- buttons in the Paste dialog box to fine tune it.  That technique would be HORRIFIC to have to do for each and every clip, however.
 
I will try the Clip Inspector equivalent you suggest, nonetheless, and post back on it.  I am imagining that it will produce a similar result to what I note above, with similar giant time required to get it right for any project with lots of clips.
 
Bob Bone
 
 

I've been kind of in and out dealing with my laundry so my head hasn't been processing all the info provided but I'm still not understanding why you can get your Now Time positioned manually. You should be able to get it accurate right down to a sample. From there when inserting the clip the front edge should be right at the Now Time marker. If it's not working something is definitely wrong.
 
I'm also trying to envision a solution that involves the Tempo Map and/or the Insert Beat/Measure and/or Insert Time Sig functions but I'd have to really reread the thread to try and absorb what's happening. Right now I have laundry to fold though. Cheers.

I had another thought too. There is a way to mess with the tempo/time sig directly on clips as well. I don't know if it will help you at all but you may find it interesting anyway. FBB did a couple vids on it...
 
http://www.youtube.com/watch?v=7VR7WkHywTo&feature=c4-overview-vl&list=PL6C8A51A85BDA4609
 
http://www.youtube.com/watch?v=weIZy_ibH5c&list=PL6C8A51A85BDA4609
 
The first one is a corrected version after one of the Bakers pointed out some stuff to him but the original is still insightful. It's a weird feature though and kind of hard to get the hang of at first. Just though you might be interested. Oh and he's actually trying to extract a tempo map from the clips to the timeline (which I don't think is what you want) but I think it can be done in reverse and there are a bunch of different ways I think this can be used.

Now Time CAN be precisely positioned, but the only way I have been able to do so is through specification of position in terms of MBT - Meter, Beat, and Tick.
 
This will not work for me, because the MBT values are quite different in the two projects due to the differences in Time Signatures between them.
 
One clip, in the original project (the guitar player's), may have an MBT value of 45:02:000, and it may correspond to a completely different value - perhaps even in the middle of a beat in MY project.  Since ONLY MBT thus far has been able to be specified for Now Time positioning, it has been extremely difficult to get a clip that was copied from his project into the correct location on MY timeline.
 
If I instead were able to set the Now Time to a TIME-based location, rather than by measures, then everything would line up perfectly every time.  Even though my project has different measures in place than his project has, the actual TIME locations are the same, for the various locations clips need to be placed.
 
The problem is in having to do the clip placements using MBT, rather than SMPTE (which uses time and not measures).
 
I hope you have not bled any colors or shrunk any underwear in trying to assist me while trying to get your laundry done.
 
Bob Bone