Thanks very much for your help, the issue was solved by removing spaces from the file paths! For posterity, here are basic instructions compiled for non-coders to install CTMK and align fly brains, with sections from your replies if that's okay:

Follow the instructions at:
https://github.com/sandorbx/Parallel-Fij...
(This will require typing a few things into a command line but don't worry if you're not a coder, it will tell you what to do).
Where it says for Windows, "Start powershell as admin", do the following:
Press Windows+R to open Run, and then type "powershell" in the text box but don't press Okay, press Ctrl+Shift+Enter.
For the part that requires Ubuntu, note that it must be installed through the Microsoft Store, which can have problems if not recently updated through Windows Updates. Then reboot your computer. https://www.microsoft.com/en-us/p/ubuntu...
When the instructions refer to the file named "Parallel_Fiji_CMTK_Registration***.ijm", that comes from a collection of files from the green "Code" button at the top of the instructions page. Download the ZIP then extract it, and move the relevant .ijm file for your operating system as outlined in the instructions.
If your confocal stack is not already separated out into different files for different channels, open it in Fiji. Scroll to a slice where you can see the brain.
>Image >Transform >Rotate >Check "Preview" >Change angle until brain is upright
Draw a box around brain but not too tightly
>Image >Crop
>Image >Color >Split channels
Select the nc82 reference channel image
>Save >NRRD >remove the leading characters that Fiji inserts, and give it a name ending in _01. Make sure there are no white spaces anywhere in the file path or name. On windows 10 the macro has the limitation that it can just read files on the internal hard drives and not from network or external drive locations.
Select the neuron stain image (e.g. GFP)
>Save >NRRD >choose exactly the same name as the reference image, but ending in _02
Check the FlyWire Gateway: https://flywiregateway.pniapps.org/ to see what template brains that site can work with, then download an appropriate one from:
https://www.janelia.org/open-science/jrc...
To run alignment in Fiji: >Plugins >Macros >Parallel Fiji CMTK Registration.
Choose an operation: Affine & warp registration
Registration parameter preset: Full Flybrain
Select desired output directory (no spaces in path names), template brain location & output directory.
Check "Show results list" and check "Reformat channel 01, 02, 03"
In the Log window, scroll to the bottom to see if it's running ("Please wait")
After a period of time (that can take quite a while), the aligned files will appear as stacks in the output directory you selected.
If troubleshooting is needed use this test data:
https://www.dropbox.com/sh/54igm0xxmtlo4...
-Place test_data folder on one of your internal hard drives directly like "C:\test_data" , use the images and the reference provided to run a registration.
-confirm that CMTK installed, open ubuntu terminal and type the command cmtk --help , after hitting enter you should see the cmtk help page.