This is just a recap of where I'd got to, along with a possible source for parts.
So off and on I'd been looking out for a couple of clock generator models that are a very close match to the one on this board.
The original clock gens that are all interchangeable are: ICS9159-02, W48C60-402 (those two have both been seen), CY2254 and CGS605 (at least, according to the National Semiconductor CGS605 datasheet). It has 3 selectable Processor Clock (PClk) frequencies: 50,60 and 66MHz output on 4 pins, along with 6 Bus Clock (BClk) outputs at /2 PClk, a Floppy Controller (FDClk) clock at 24MHz, a Keyboard Controller (KBClk) clock at 12MHz and two copies of the Reference clock (REF0, REF1) at 14.318MHz.
Some hunting around found 2 clock gens with almost identical pinouts, which had more options for PClk, including 75 and 83MHz. Those are the PLL52c59-14A and the ICS5159C-14. There are two pinout differences compared to the standard chip:
1) Pin 5, the Output Enable (pull high to enable outputs) input has become the Turbo/FSel2 pin. Pulling that pin high gives the same frequency options as originally (with a bonus 55MHz in place of a test mode). Pulling it low gives 4 new frequencies, which are slightly different between the two alternate clock gens. The PLL option has 4 options for synchronous or asynchronous modes at 75 and 83Mhz. As far as I know from skimming the Intel datasheets, the chipset on the Tyan S1564 doesn't support asynchronous modes, so they're not useful in this case. The ICS option has 4 frequencies: 62,68,75 and 83MHz.
2) Pin 25, KBClk. On the original this is a 12MHz clock to the KBC. On both the alternate clock gens it's a 48MHz USB clock.
On the face of it, directly swapping them in would stop the KBC controller from working, which the BIOS would probably flag as a failed KBC. So it seemed like it would start getting messy to correct this, having to either introduce a separate KBClk, or take the USBClk and run it through a couple of flip-flops to get USBClk/4 and feed that in to the KBClk pad.
Fortunately, with a bit of following the traces, and some measurements by Sphere, we found that the Tyan has a 0 ohm link that can be used to select which clock actually drives the KBC. It can select between either pin 25 (the 12MHz part on the original clock gen, which becomes 48MHz on the alternate parts) or pin 27 (one of the 14.318MHz reference clock). It turns out that the KBC (or at least the one that Sphere tried) worked at 14.318MHz.
So if one of the alternate chips is fitted, and the 0 ohm link moved, then the board should work. That leaves just the question of how to select the extra frequencies. R48 (4.7k) pulls pin 5 high, so pin 5 can be connected directly to ground and only pull about 1mA through R48. There are several options to pull it low. Pin 4 is a ground pin, so pin 5 could just be shorted to pin 4, although that means the original frequencies can't be selected. If a jumper header is fitted between them then there will then be three jumpers, giving 8 possible frequencies. I'm not entirely happy about hooking on to a ground pin of the clock gen, so perhaps hooking on to the ground via/pin near the other frequency jumpers would be better.
The attachment Tyan_S1564D_Clock.jpg is no longer available
Short version of steps:
1) Remove old clock gen
2) Fit new clock gen
3) Move 0 ohm down one place
4) Fit jumper from pin 5 to Ground.
And that should be it.
Personally, before trying this, I'd want to check the KBC was happy at 14.318. I'd keep the original clock gen in place and lift pin 25 to disconnect the KBClk pin. Then check that the BIOS halted with a failed KBC message. Then move the 0 ohm link, to connect the 14.318 reference to the KBC, and check everything to make sure the computer was stable.
Of course, all this is useless without being able to get parts. Sphere didn't have any luck with the couple of parts houses he tried. I hope this doesn't fall afoul of the no trade rules, but I did find a couple of possible sources for the ICS9159C-14. They're both AliExpress sources with very little feedback, selling used parts, so it's likely to be pot luck as to whether they are exactly the right part, not fakes, and if they actually work. But may still be worth a punt if you're feeling lucky:
https://www.aliexpress.com/item/1005002233119924.html
https://www.aliexpress.com/item/4001246130137.html
Other useful links:
CGS605 (compatible with standard clock gen) datasheet: http://pdf.datasheetcatalog.com/datasheet/nat … or/DS012491.PDF
PLL52C59-14A: http://www.ryston.cz/petr/mirror/www.phaselin … s/PDF/5914a.pdf (can be useful to search for PLL52C5914ASC, PLL52C59-14ASC)
ICS9159C-14: https://pdf.dzsc.com/9C-/ICS9159C-14_1191261.pdf (can be useful to search for ICS9159CM14, ICS9159CM-14)