Long Piece and Markers trouble

I can't repro a problem dragging three, long MIDI clips - or groups of non-contiguous clips - out to 45 minutes. Have you tried cut-paste? Or maybe disconnect the outputs of the tracks from whatever soft synths they're referencing, and point them to a hardware port if possible.
 
Personally I would keep the two projects open at the same time, but what you want to do should not be a problem.

Ah, ok, the problem is not when I drag the clips out, it's shortly thereafter. I drag the clips out, and everything seems fine. Then I start working and it crashes right away. So I don't think cut-paste will change that.
 
I've started using two separate projects. Not as convenient, but I'll get used to it. However, now I'm reluctant to do something similar in another piece.
 
This other piece is a mash-up of about 50 songs. All the original songs have different tempos. The first step has been to lay down a dummy track for each song I'm using in its own track, as I'm just using little parts of each. How I'm doing this right now is to solo a track, set the tempo to the original song's tempo, and inputting the midi notes at the right tempo. Obviously, if I were to go to another track I've already done, the tempo will now be wrong, because I change it for each song I'm inputting. Right now it's just about getting the raw material into the project, but I'm going to have to figure this out. My idea is to create a marker for each tempo I'm going to be using, each about 5 minutes out. Change the project's tempo at each marker, and drag the songs out to the correct tempo section. In addition, I want markers to delineate workspaces, such as "Raw Materials", "Final piece", whatever. 
 
What I really need for this is something like Excel, where there can be multiple pages within a single worksheet. I'm trying to mimic that with these markers, but now I'm worried that I will be inviting lots of crashes based on my experience with the previously discussed project. Fortunately, this piece is all piano, so I don't have multiple instruments to deal with.
 
If this is confusing, let me explain again:
Bar 1
Marker: FINISHED PIECE
Tempo: Will vary
 
Bar 999
Marker: RAW MATERIALS
 
Bar 1000
Marker: 120 BPM
Tempo: 120
Contains all the songs that were originally 120bpm
 
Bar 2000
Marker: 140 BPM
Contains all the songs that were originally 140 BPM
 
etc....
 
How would you go about this? I definitely do not want to have a separate project for each raw song, because there are about 50 of them, and the finished piece is going to be organically weaving them together, not like a medley where each song gets it's own section and played through. So having a bunch of separate projects would constrict the creative flow I'll need. Ideas?