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Wow, that is the MOST comprehensive reply ever. Thank-you Thomas!
After all, this thread will hopefully provide all the necessary info. for others to succeed, right?
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So, I downloaded the latest Greaseweasle (1.19) I was using 1.18, and the latest GUI (Graphical User Interface)
I set GUI parameters exactly as per your screenshot and wrote a known good .hfe file, C1-Monstermaze , that boots reliably on the Gotek, to a new disk, in my 35 track, Shugart A400 (5¼")
(I chose Monstermaze because I know that the progam resides on the first 3 tracks of the disk)
EDIT: first 4 tracks, 0 to 3...

This newly created disk doesn't boot.
I noted that the separated clock from the floppy drive is +-135Khz, whereas the clock on the Gotek is exactly 125Khz...

I will have to verify the spindle RPM, as I can see that someone has "twiddled" the potentiometer on the motor control circuit board.
It is my understanding that the Greaseweasle generates the data clock frequency of 125Khz, which is "parameterised" in the .hfe file itself. It is this freuency that is used to modulate the magnetic flux on the disk.
I'll need to investigate why this disk in the drive, connected to the data separator, generates a 135Khz clock, as oposed the required 125Khz. (measured at the data separator during a disk "read")
...

Wow, HxCfloppyEmulator is able to 'visualise" the magnetic variations of the tracks on the disk!

H.

Could the drive be spinning at a different speed when attached to the OSI than it is when attached to the Greaseweasel? If the speed was the same, then a signal written at 125 kHz would be read back at 125 kHz, wouldn't it?

Anyway, for the record, that Monster Maze program actually resides on tracks 2, 3, and 4 of the disk. Tracks 0 and 1 really contain OS-65D, with the Monster Maze game replacing (part of) the BASIC interpreter. That was the easiest way for me to make a "self-booting" game disk. BTW, there is still a directory and some 65D software on that disk if you look at it after booting 65D. Some of it you might find interesting.

EDIT 9:17 PM: No, I was wrong about how the C1-MonsterMaze.65D disk is structured. Track 0 does contain the disk drivers from OS-65D, but the game is stored on tracks 1, 2, and 3. Still not the "first three" tracks of the disk, but not what I thought I remembered either. But there are indeed a 65D directory track (normally ignored) and some program files.

Thomas, yes, the clock "should" be exactly what was written by the Gotek, provided the spindle rpm is constant... The spindle motor speed is controlled by the floppy drives electronics, and not by what it is "connected to"...
However, I will check the rpm when when the drive is connected to the gw, versus the 610.

Also, what I should have said is, I do not know how the tracks are constructed, but what I do see, when booting C1-Monstermaze, is the track indicator on the Gotek step to track 3, never any further.

...more testing...

H.

Yes, you are correct that the MonsterMaze disk reads only to track 3 (which is the fourth track) when booting. I edited the message (which was from me, not Thomas) to correct my mistake. I definitely do make some.

It's me, Thomas
Yes, the "clock" should be the same after write, whatever the spindle speed is.
However, if the spindle is above 300rpm, you might face a different problem. The OS65D tracks need a certain time/space and if the rpm is too high, data will be written across the disk index area. This will cause tracks not to read in correctly.

Speed differences on the SA400 do only make sense, if the Head load mechanism was or was not correctly engaged during read or write.
No proper head load will have effect on head friction to the disk and a slightly higher rpm.
Also head load timing can be critical, if the head load solenoid is a "kind" of slow due to stickiness or other restrictions or due to failing driver electronics. More trouble shooting ....., yes it's a 45 year old mechanical drive ....

All good information, thank-you!

More testing... which is how we learn, and retain newly acquired knowledge.

I see similar clock speed differences / inaccuracy with a brand new 1.44MB stiffy drive.
I had to perform a solder bridge to get pin 12 "jumpred" (un- soldered pin 10) so as to have the drive connect as drive 0, with an un-twisted cable.
(No physical drive-select jumpers on the SAMSUNG-SFD321B I'm afraid)
That had me scratching my head for a while, until I decided to open up the "brand new" unit, thus voiding my warranty.

H.

seriously, that's not possible. Then something must be going wrong with the frequency measurement. Maybe you can provide scope captures of the write and read data of the 3.5 inch drive.

Have you tried to connect the 3.5" drive to the OSI, to see if you can boot from that? It may not be quite period-accurate, but it's not that far off, it's the same basic technology. And you wouldn't be limited to 35 tracks. I know that some people have done it successfully.

To answer your question Danny, yes, I've tried booting OSI with the stiffy drive with C1-Monstermaze.hfe. - No boot...

So, for sanity's sake, I wrote C1-VictorySoftware.hfe to the Gotek, using the Greaseweasle, with settings as shown in the screen-shot below:


Then, I read this newly written image, from the GoteK, using the Greasewesle, calling it mydisk49.hfe.
See Greasewesle settings below:


I converted mydisk49.hfe to mydisk49.65D, using OSIHFE.EXE.
Using WinOSI emulator, mydisk49.65D boots perfectly, which means that the Greasewesle is working correctly. Right?
See below:


I then connected the Gotek to the OSI, and mydisk49.hfe boots fine!
(Greaseweasle and Gotek playing nicely together...)

OK...

So then, using exactly the same settings as used to write to the Gotek, I wrote C1-VictorySoftware.hfe to the stiffy drive.

The stiffy disk (with C1-VictorySoftware.hfe) does not boot on the OSI , (neither does C1-Monstermaze, or mydisk49.hfe)

...Time to compare signals:

I connected the 610 & Gotek, using C1-VictorySoftware.hfe, then C1-Monstermaze, then even mydisk49.hfe!
All 3 boot ok.!
I scoped the separated clock and data signals, pin 2 and 3 on the ACIA.
The Gotek clock is very stable, at 125 Khz, and data "seems" correct, because all three boot!
This means that the Greaseweasle is CORRECTLY interperting the instruction in the .hfe file, and, the Gotek ouputs exactly what is instructed!!!
See below:



So then, I connected the Stiffy drive to my 610, with the same C1-VictorySoftware.hfe on it and scoped the signals...
The clock is not stable, the frequency is "mostly" 128Khz, and vaies, up to 129.75 Khz, down to, as low as 106Khz ! No boot!
See below:


Why?

I tried, many, many times, writing .hfe files to the stiffy disk, with every possible combination of "settings" I could try.
(brand new Verbatim, never before used, 1.44MB disk)
No boot.

I am at a loss..., Maybe the stiffy drive (EBAY ) is faulty?

Maybe the one-shot timers on the 610 can be "adjusted" to accept this frequency "variation", yet still permit the Gotek to boot?
As I mentioned before, I agonised over setting them as accurately as I could.

... yet MORE testing...

Edit:
Does anyone have a SINGLE TRACK .hfe file that will boot?
Maybe it is the head "stepping" that does not work correctly on the OSI?
(grasping at straws here....)
Is there any OSI software that I could use to "manually" step the stiffy read/write head?

H.

Does anyone have a SINGLE TRACK .hfe file that will boot?

I constructed this file to do exactly that. When booted, It will simply display

THIS MESSAGE DISPLAY IS FROM CODE THAT'S LOADED FROM TRACK ZERO

(a message which was carefully phrased so as not to split words between lines).

But if track zero were loading, Thomas's recent utility, or the ROM code at $FC06, would show it. So my guess is this won't work. But you may as well try it.

(This is a real ZIP file.)