MacOS – can i use migration assistant to migrate files to a secondary drive

Migration assistant will copy files into expected places on the disk so ~/Library ~/Documents etc and is only meant to be used when installing OSX.

If you want to copy to one directory don't use Migration Assistant. Instead

1. Install OSX from scratch and create a new user (for ease if you have multiple users create them in the same order as before so that their UIDs match) - or just keep the target running current OSX.
2. Connect Macs via firewire and boot up old Mac in Target Disk Mode
3. The old disk is now seen under /Volumes
4. Copy files onto new disk as you want

If step 2 fails then you need to take the disk out of the old Mac and put iy in a USB or other external disk caddy. Then it might work. If the disk is corrupt then look at disk recovery tools or firms.

Also not really an answer but more a practical approach.

Another idea that requires manual work. I did this with a Macbook Pro and a MacPro 2006:

• Boot your old MacPro into Firewire Target Mode (yes this works with "T" on power on).
• Connect it to you new MacPro with a FireWire cable.
• Mount all harddiscs
• Copy over all data you need, but leave out the Library folder in your old homedirectory.
• Do a fresh install of your favourite software, that is quicker and safer that copying them from the old MacPro or a TimeMachine Backup. You will definitely miss important files. (just my experience with MS Office)

Positive effect of this: you trashed all old things you really do not need. :-)

I even go a step further - On my old MacPro I set all files and directories I want to copy on a red label in the finder. When mounting the harddiscs, I immediately see what is important and needs to be copied. :-) And as a reminder of which software I will need on the new machine, I set the finder label "green" to all applications I will need on my new machine.