can do a full backup and do a restore after a clean install on the SSD.
But otherwise a clone is by perfect definition a full on clone.
Clone might be better.
me personally, I would just backup important files to cloud leaving all the stuff that can easily be redownloaded and installed again alone, then just doing a clean install on the SSD and reinstalling stuff.
But if you have games, a lot of them could have very different save file locations that you would have to track down.
so you should just probably wipe the ssd clean, then do the clone.
fairly simple.
and free space shouldn't matter since that would just be free space either way no matte what on your storage.
I've personally been running on a dual drive setup for a long time now for the specific reason of not having to bother with cloning and whatnot since the only thing on the SSD for me is just the OS and main applications and all long term files and games go onto my HDD with only short term stuff that I'm messing with in the moment being on the SSD.
So that in the event that the SSD starts to fail, or I get to a point where I feel like I just need to hit the reset button and start fresh with a clean install of Windows, everything important is already on a different drive and in the cloud.