@eharmon - sure - happy to help!
I was thinking about this problem last night, and coming at things from a different engineering direction, focusing on the CLK-02 (or CLK-0?) IC might be helpful. We know certain things about it. It is the clock synthesizer (in the lower right-hand corner on the original Thunder/24 board) -- and it's labeled CLK-02. Instead of trying to iterate on timing, it might be faster and more certain to characterize the behavior of CLK-0x.
I have posted historical clock frequencies in other posts. But...the main thing of interest is connecting the CLK-02 output frequency to the sRsrc configuration/setup value -- that first byte after the length. The first point of verification is that if you change the value and the clock changes, then it's a known entity.
After a certain point in time, 60Hz configurations were out because of fluorescent lighting interference/oscillation (and vendors like Sony/Hitachi switched to 75Hz). So, SuperMac would have tried to avoid implementing future configs at 60Hz. The transitional point for this change was at the Series III boards (Spectrum/8 III and Spectrum/24 III).
-Looking at the sRsrcs, the CLK-02 values (1st byte after the length in the sRsrc, as in my earlier posts) are as follows:
$0c: 1024x768 60Hz = 64Mhz
$0d: 1024x768 75Hz = 80Mhz (various timings -- SuperMac, RasterOps, etc.)
$0e: 1152x870 = 100Mhz (various 21" configs)
$1f: 1280x960 = ? If it's 75Hz, then it's likely going to be in the 129Mhz range - maybe? If it shipped, it should hopefully be 75Hz. If 60Hz, then it will be less. Is it indicated as 60Hz in SuperVideo 3?
However, with its custom ICs, SuperMac would have planned for headroom for larger configs in CLK-02 (or maybe they had to spin it) and there were larger displays available at the time -- just not characterized or integrated as product SKUs. For 12890x1024, it could have been a 60Hz issue or also a next-gen marketing decision to get people to upgrade to the Thunder II, etc. boards. Either.
The sequential implications of the resolution progression are that $0f is the next in the sequence and 1280x1024/960 is the next step. Since the
shipped clock value for 1280x960 is $1f, then that must mean that $0f is for something else...and that something else could have been 1280x1024 -- maybe at 60Hz, which is why $0f wasn't used -- or it just wasn't right (again pointing to a possible spin if the Thunder II/IV have updated CLK ICs). The odds point at $0f for 1280-something.
Anyway -- assuming the first byte controls the clock, if someone would like to scope the output of CLK-0x to confirm the frequencies -- it should be possible to match the above known configs. Then, the next logical thing to do would be to
plug in sRsrc values of $0f-1f to characterize the output frequencies of the CLK chip. It doesn't matter what the screen shows -- don't even connect a monitor -- just look at the frequency output on CLK-02. And, knowing the frequencies, it should then be simple to set up the modified timing (and choose the best clock value). Supported configs may go higher than $1f -- that's also something to test.
As above, the Thunder II and Thunder IV boards may have an updated CLK IC. I haven't looked/don't know. If so, then it would be good to characterize it vs. the CLK-02 on Thunder/24. And, if it's a new version, then the spin might have been for 1600x1200 support (not available in 1991 when CLK-02 appeared), since that was the max config.
Also -- one edit -- looking at the earlier SMT discussion of x16, x4, etc. It looks like SMT is x8, where there are 8 pixels displayed for a visible area of 160 at a horizontal resolution of 1280 that adds up to an HTOT of 201. So, if correct, each change to a blanking value should move the margin by 8 pixels vs. 16 or 4.