here's a screenshot of all my percussion part being somehow linked together

I believe that your percussion parts need to be on different channels. I could be wrong, though, since I don't use percussion.

For the last, select the empty measures, and then choose MM Rests > Create.

Hi Mike, thank you for your answer. I've tried to change the channels in the Score manager, but unfortunately if I change one staff to one channel, then all the percussion channels get assign to the same... As for the MM rests, when doing exactly as you say, nothing changes and the rests aren't created.

I've noticed another issues that might be linked. I cannot create any notes, anywhere in the score. When clicking to create a new note, Finale doesn't allow me to do it. I don't get an error message, but rather an error sound.

* Correction, I can indeed insert new notes, sorry about the confusion

1. If you started your Finale score by importing MIDI, that may affect some of the obstacles you are facing.
2. If your DAW (if that was your original source) can export XML, you may want to use that to create a second version of your Finale score to see if the results are better.
3. For your copy/paste problem, try importing the MIDI excerpt into a separate Finale file and then copy and pasting form one Finale file to (a copy of) your master Finale file.
4. Can you post a screenshot of your Score Manager here (at least the part that shows your multiple snare parts) to help us see how the various instruments and MIDI channels have been assigned?

Finale is a very flexible program, but even after (how many?) 30 years, I recall it was a challenge to start learning. You are a brave soul, and I hope your patience will be rewarded soon.

Hi Adrian, thank you so much for your help!! 

I imported the project from Logic as a XML file, and not MIDI. Everything was fine for all other instruments (Horns and Trumpet weren't showing abbreviated names, but I fixed in in the Score Manager), only the percussions had this issue. 

If I understand correctly your third point, that is what I am trying to do for copy/paste (I couldn't find a way to import MIDI straight in the master session anyway). When copying it to another Finale file, it still won't show it my main file. 

Here's my Score Manager! Hopefully your experienced eyes will spot the issue here! And thank you very much, it is a quite challenging software when first using it! It certainly troubles my patience! 

At present you are using Finale's equivalent of MIDI sounds rather than Garritan Sounds, considered more realistic by many.

The way Finale likes to assign sounds (as well as set you up for Human Playback) is for you to choose the instrument (Aria/VST or SoftSynth) in the leftmost column. The second column from the left lets you choose a Name for the instrument but does not identify the instrument to Finale.

What would happen if you chose different instruments for each of your snares in the leftmost column? I always suggest trying these things on a copy of your original file just in case you want to retreat.

MIDI often puts percussion sounds into channel 10, although Garritan (Aria) can put percussion sounds in any slot.

I don't actually have the Garritan sounds (I'm using the trial version at the moment). I have tried to change the sounds to each instruments, but same issues as before, it just changes for all. It is like they are acting as one instruments.

Romain Quessaud,

Another thing to try:

Selection Tool.

Select only one staff.

Utilities menu > Change Instrument…

Change the instrument to any instrument (the actual instrument does not matter; this is a test).

* If you use the utility to change the instrument of only a single staff, do the other staves change instrument, too?

I mean, if the other staves do not change, then you have a way for “breaking the linking” between the staves.

When the staves have become “un-linked”, you can freely change channel for each staff.

Hi Peter, 

That worked!! Thank you so much, such a relief.