Probably the super I/O chip IF a mouse is not working on that header. Or is it?

Well, that's what I was afraid of, hopes for burned trace were low anyway.
My understanding is you should read 5V on VCC, DATA and CLK.
You see, I don't have original cable with connector so I was about to rewire one I have and that's why I was figuring out the pinout.
I can try to finish the job, but I doubt it will work.

Would fried super I/O chip also explain non-working floppy drive?

Sucho wrote on 2024-05-08, 21:38:

Would fried super I/O chip also explain non-working floppy drive?

It sure would but I find it odd that you've managed to kill that chip so properly with just one short on PS/2 port. IIRC the design is pretty much identical to AT, which is OC/OD outputs and pull-up resistors. Short to GND does nothing (other than stopping the port from working), short to VCC migh kill the outputs but it's not 100% certain (especially for brief shorts). If the PSU tripped then you've most likely shorted GND and VCC, that would actually spark. But it shouldn't have taken out the chip. Is there still 5V on the VCC pin on that port? How about GND, also present?

I fried a ferrite with a short and died a burning death.
Check any component on the CLK and test for shorts, res too high etc.

Good news, everyone. It just works. I could have sworn that I have read 5V on that CLK pin before.

Nexxen wrote on 2024-05-08, 23:33:

Check any component on the CLK and test for shorts, res too high etc.

Deunan wrote on 2024-05-08, 23:22:

Is there still 5V on the VCC pin on that port? How about GND, also present?

I checked as you guys suggested and could not find anything else out of place.

PD2JK wrote on 2024-05-08, 20:52:

Probably the super I/O chip IF a mouse is not working on that header. Or is it?

So I went ahead and finished the wiring, loaded ctmouse and voila. Mouse works. Clicking.. Double clicking.. So can confirm the pinout from the link in OP.
Floppy was still unresponsive, so I swapped it with my other one and it works too. It came with a case and I never really got to check it out before I guess.

So there's that. Thanks everybody for chipping in!

Sucho wrote on 2024-05-09, 18:05:

So there's that. Thanks everybody for chipping in!

No, go break something else and let us figure it out 😀

This is great news!! Have fun with it.

Nexxen wrote on 2024-05-09, 18:58:

No, go break something else and let us figure it out 😀

Haha, there is still 8-pin usb header to wire 😁
Checked voltages on the outside pins and it looks like it's this version:
GND .......... VCC
VCC .......... GND

Without fireworks this time. I mean, so far. Haven't attempted to wire it up yet.

Wired up the USB header and it would not show up in Windows 98SE. So I checked the BIOS and it is disabled there. So I enabled it, still nothing.
Checked BIOS again and seems my settings are NOT being saved at all, except for real time clock.
Immediately thought bios eeprom is worn out (which would be fun for sure), but the board uses DALLAS DS12887.
I tried to dig around and found out it's not just a simple battery and some boards rely on it's chip to store (some?) bios settings.
After removing it, pc would not boot at all.

Could DS RTC be the culprit?

Sucho wrote on 2024-05-11, 11:20:

Wired up the USB header and it would not show up in Windows 98SE. So I checked the BIOS and it is disabled there. So I enabled i […]
Show full quote

Wired up the USB header and it would not show up in Windows 98SE. So I checked the BIOS and it is disabled there. So I enabled it, still nothing.
Checked BIOS again and seems my settings are NOT being saved at all, except for real time clock.
Immediately thought bios eeprom is worn out (which would be fun for sure), but the board uses DALLAS DS12887.
I tried to dig around and found out it's not just a simple battery and some boards rely on it's chip to store (some?) bios settings.
After removing it, pc would not boot at all.

Could DS RTC be the culprit?

Yes.
But... are other settings being saved? Like changing COM1, LPT ... ?
There is a hack to put an external battery on the Dallas.
https://www.youtube.com/watch?v=IbiczYoVncQ

https://www.youtube.com/watch?v=svPNxILeQEw

Tried also disabling some random settings as COM and LPT ports. FDD check on bootup. And some others. Only real time clock seems to be saved.

Does the board have a genuine Dallas 12887 fitted?
There are minor differences between Dallas 12887 and other brands (Odin etc.) as well as other Dallas models - for example the DS12885 and DS12887A both have an RCLR pin, which will reset the saved contents when grounded (but not the calendar).
Boards that were designed specifically for the 12887 would often leave this pin grounded because for that RTC it made no difference.

jmarsh wrote on 2024-05-11, 13:50:

Does the board have a genuine Dallas 12887 fitted?

Seller sourced it from aliexpress, so difficult to say if genuine. But it says DALLAS DS12887 and all.

Nexxen wrote on 2024-05-11, 11:42:

There is a hack to put an external battery on the Dallas.

First, I used the nail and hammer to make drilling easier.
Used ordinary drill bit to strip the casing. Careful not to drill too deep, managed to expose contacts just enough to solder cr2032 housing cables onto.
Upon exposing the contacs I read voltage of around 0.34V (on the internal batttery?)
I am pretty sure I butchered the soldering job, but it works! Thank you. And cheers to the dude who made the video.
Now onto frying something else by plugging in usb.

Good news everyone! Both USB ports seem to work, tested with mouse and flash drive.

Sucho wrote on 2024-05-11, 15:33:

Good news everyone! Both USB ports seem to work, tested with mouse and flash drive.

All good in the end. I'm happy it turned out to be just a learning experience.
If you want you can watch some more video by Necroware to learn even more stuff that will come handy someday.

Cheers!

Good to hear, have fun with it!