I believe a solution now that you already semi-reinstalled once, could be to go in and manually retrieve your VM's from a live media boot (if you didn't already delete them), i.e. using any other Linux live distribution. Salvage your '/var/lib/qubes/' folder, where all your VM data resides. I.e. copy it to another drive.
But preferably another disconnectable drive or external drive, just in case the fedora bug that affects other partitions during install is still there in fedora 25 for Qubes 4 (I'm not sure if it is, I know it's present in fedora 23 which Qubes 3.2 is based on).
basically, make a fresh install after salvage, and then drag and drop the specific VM content img files, in new fresh created VM's for the specific purpose, overwriting the new empty img files with your old ones. Then it "should" work. Mind you, "should", as in, I believe so, but not certain.
Finally, you might want confirmation from someone who actually did this before, or someone who knows the system better than me. This is what I would do as a last resort, last ditch attempt to save my data, if I were in a situation that I could not recover from. I have not done it before my self, so I cannot confirm if it works. But hypothetically, it should.
You would have had to edit grub and remove the hide all line to be able to enter passphrase. https://www.qubes-os.org/doc/usb/
WHat you can do for keyboard if you have a ps2 port is use a usb to ps2 adapter.