My concern is copy/pasting from two seperate scores into one composite score.  The scores are multi-metered.  Here we go.

Score 1:  Is a midi file that I saved into Sibelius. 
Score 2:  Is the percussion book written.
Score 3:  Composite of Both (ideally)

I set up Score 3 with the appropriate instruments and staff assignments.  My problem was that if I hit Crtl + Click, it highlights the entire work (either Score 1 or Score 2), and then the number of staves and measures don't line up, so it doesn't paste.  If I hit Shift + Click, and highlight each individual line, the measures do not retain the metric value (3/4 to 4/4 to 3/4 etc..).  Is there a better way to set up this up initially so I don't fuss with this in the future?  Thanks.

If you're going to paste music from one score into another, it's best to make sure the measure numbers, key sigs, and time sigs all match. It may be easier to work from two scores rather than three. If score 1 or 2 are based on the VDL template, than choose one of those to paste in music from the other. If neither are based on a VDL template, then score 3 would be the way to go. Start by just getting score 1 into score 3, ensuring all time sigs and rehearsal marks line up as you expect them to. Once that's satisfactory, close score 1, save score 3, then open score 2 and do the same.

If you triple (or quadruple) click a single staff in Sibelius, the staff will become highlighted for the whole score. Then shift click successive staves below it to add them to this selection. Once you have the correct amount selected, select ";copy"; so you can then go into score 3 and paste it.

Score 2 has the vdl templates set up already.  Score 1 is just the midi I saved as a .sib file.  You're suggesting it be best to copy score 1 to score 2? Just add the instruments, and go through the copy past process?

Yes, I think that's what he's saying...  First, dupe #2 so you have the original backed up.  Then add in the staves for the other score, and copy paste them in.  That should give you a composite with the least amount of headache, by far.

I think that's what I'm saying. :)

I'm running with the assumption that score 1 is probably your wind book, and (perhaps) was written with Finale, and you're trying to import it into your already-written VDL percussion score (score 2).

So the copy-paste, would only apply to staves that you want to [b]add[/b] to score 2. Don't paste over anything you've written and want to keep. So before you paste, be sure you've created the appropriate new staves into score 2 (i.e., flute 1, flute, 2, cl. 1, cl. 2, etc.).

On another note, if you're score-swapping like this, often you'll get better results by importing a saved Music XML file as opposed to a MIDI file. There may be cases where you need to use a MIDI file, but if your other score originated in Finale, you might want to see if it can first be exported to a Music XML file (which is built into the last few versions of Finale). Sibelius will then retain things like articulations, hairpins, dynamics, slurs, etc.

Hope I haven't made things more confusing...i sometimes have a way of doing that. ;)