pfi tfx_00.0.raw disk1.pfi
pfi disk1.pfi -R 1 -r 500000 -p decode pri disk1.pri
pri disk1.pri -p decode mfm disk1.psi

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Hello,
I've managed to get the Kyroflux stream files from my original SpaceQuest one disk converted to to PSI images which retain all the copy protected info and thus can be mounted and used in PCEmulator. :D Rocking.... 

Here's the details. Many thanks to Hampa and his PCE project. (http://www.hampa.ch/pce/download.html)

You can find the latest version of PCE with Kryoflux (and some
other) patches applied here:

http://www.hampa.ch/pub/pce/pre/pce-201 ... -win32.zip
http://www.hampa.ch/pub/pce/pre/pce-201 ... pfi.tar.gz

In particular, you need the pfi.exe, pri.exe and psi.exe
utilities found in the first archive in the bin directory (I'm
assuming your doing this under Windows).

First we convert the Kryoflux raw streams to a PFI file:

$ pfi sq1-00.0.raw disk1.pfi

Note that I had to rename the files you sent me. Files like
sq100.0.raw won't work because pfi.exe will assume that this
is track 100, side 0. Also note that you need to run this
command just once, with any one of the raw streams as first
parameter.

Now we have a PFI file. This contains basically the same
information as the Kryoflux raw streams, but in a more
convenient format. You can inspect the contents like this:

$ pfi disk1.pfi -l
TRACK 0/0: DATA=249820 CLK=24027428 LEN=24076837 IDX=6 RPM=299.3844
TRACK 0/1: DATA=255339 CLK=24027428 LEN=24077243 IDX=6 RPM=299.3793
TRACK 1/0: DATA=227983 CLK=24027428 LEN=24077246 IDX=6 RPM=299.3793
TRACK 1/1: DATA=243318 CLK=24027428 LEN=24077389 IDX=6 RPM=299.3775
...
TRACK 79/0: DATA=236877 CLK=24027428 LEN=24078030 IDX=6 RPM=299.3695
TRACK 79/1: DATA=243508 CLK=24027428 LEN=24077312 IDX=6 RPM=299.3785
TRACK 80/0: DATA=200830 CLK=24027428 LEN=24077605 IDX=6 RPM=299.3748
TRACK 80/1: DATA=195465 CLK=24027428 LEN=24077916 IDX=6 RPM=299.3709
...

Here you can see that the image contains 5 revolutions for each
track (resulting in 6 indices). The image was made with an 80
track drive at 300 rpm.

pfi.exe can also do some simple (very simple) analysis of the
disk contents:

$ pfi disk1.pfi -p analyse
Track 0/0: MFM 495 KHz
Track 0/1: MFM 496 KHz
Track 1/0: MFM 494 KHz
Track 1/1: MFM 492 KHz
...
Track 79/0: MFM 500 KHz
Track 79/1: MFM 494 KHz
Track 80/0: FM 201 KHz
Track 80/1: FM 195 KHz

This shows you what pfi.exe thinks is on each tracks. As you
can see, all tracks up to 79 are detected as MFM at (about) 500
KHz. This is as it should be. Tracks 80-83 are unformatted and
produce random results.

Next we convert the PFI image to PRI:

$ pfi disk1.pfi -R 1 -r 500000 -p decode pri disk1.pri

PRI images contain raw bits, basically the same content as a
PFI but with the flux reversal pulses converted to bits. The
above command does this at 500 KHz for the first revolution (-R
1).

Finally, we convert the PRI image to PSI:

$ pri disk1.pri -p decode mfm disk1.psi

PSI images contain the disk content at the sector level,
basically the same information as a common raw dump like the
one you included in the archive you sent me, but with extra
information about irregularities. This PSI image is what PCE
can use. You can inspect the contents like this:

$ psi disk1.psi -L
0 0 0 0 0 1 512 MFM POS=1286 
0 0 1 0 0 2 512 MFM POS=6518 
0 0 2 0 0 3 512 MFM POS=11747
0 0 3 0 0 4 512 MFM POS=16976
0 0 4 0 0 5 512 MFM POS=22184
0 0 5 0 0 6 512 MFM POS=27433
0 0 6 0 0 7 512 MFM POS=32680
0 0 7 0 0 8 512 MFM POS=37905
0 0 8 0 0 9 512 MFM POS=43144
...
6 0 0 6 0 1 8192 MFM CRC-DATA POS=1288 
6 0 1 6 0 2 1024 MFM CRC-DATA POS=7048 
6 0 2 6 0 3 1024 MFM CRC-DATA POS=12808
6 0 3 6 0 4 1024 MFM CRC-DATA POS=18568
6 0 4 6 0 5 1024 MFM CRC-DATA POS=24328
6 0 5 6 0 6 1024 MFM CRC-DATA POS=30088
6 0 6 6 0 7 1024 MFM CRC-DATA POS=35848
6 0 7 6 0 8 1024 MFM CRC-DATA POS=41608
...

As you can see, there's weirdness on track 6/0. The game checks
this track to verify the disk.

I have just done the steps above and the resulting image works
perfectly for me.