|"...it's sitting in the middle one of total 5 PCI slots but I've tried it in others too...."|
That was a good thing to try.
"I even changed all the stuff using IRQ 11 to use IRQ 10 instead to see if it helps but no luck."
That was a good thing to try, there may be more cards that can use IRQ 10 rather than 11, but...
You have only 1 free usable IRQ.
I don't think the USB 2.0 card will install unless it can get two IRQs that it can use, from the same slot. It's hard to determine what IRQs the PCI card can use, unless that's in it's specs (look up the specs for the NEC chip model ?). You usually can't specify IRQs for PCI devices in Device Manager; for ISA devices, you can often choose from two or more IRQs, but you often need to switch off Use automatic settings to do that.
Most cards will not use IRQ 7 even if it's available - that (for LPT1) or IRQ 5 (for LPT2) is used by a parallel port, but most printers don't need to have an IRQ assigned to them in Win 95 and up unless you're using it in true Dos. Sometimes on older systems you can set the sound to use IRQ 7 - IRQ 5 can be used by many cards.
Devices built into the mboard often use the same IRQ, no problem, although the video slot usually uses a different IRQ. Is the network adapter built into the mboard ?
"the bios won't let me disable the PS/2 mouse which indeed uses IRQ 12"
You must not be using a PS/2 mouse. Use a serial mouse (connected to a Com port) or better still a USB mouse (all USB devices use the same IRQ, or one of 2 IRQS for a USB 2.0 controller port).
Then you must disable the PS/2 mouse in the bios, if you can - usually you can.
Some bioses do not release IRQ 12 for other use even if you try all possible ways of doing so; some bioses will auto assign it to PNP use; in others you have to change a setting to do that.
"Actually I also tried to disable the COM ports and the bios says they are disabled but Windows says they are still using IRQs 3 and 4."
If you are not using the Com port IRQs, even for an internal Dial-up modem which looks like does not apply, you may need to go into Device Manager and Disasble the Com ports - that should free up IRQ 3 and 4.
"Also disabled the onboard USB - no difference."
If you can't get the USB to use an IRQ other than what the other devices that are built into the mboard that are using the same IRQ are using, then it's not going to help to disable the onboard USB.
On my Epox mboard, which does not have anything except the USB controller built in (other than a parallel port, two USB ports, two Com ports, two PS/2 ports), in 98SE, the onboard USB's IRQ is shared with the network card (9) (that may not be ideal) and the video's IRQ is not used by any other device.
(There's a thought - can you get some device that isn't using IRQ 11 (or 10) to share IRQ 9? )
In a situation like that...
In older bioses like yours, there are often two settings for USB. You have to disable both, or the more important of the two, to free up the USB's IRQ, then you must load Windows at least once in order for Windows to recognize the IRQ the USB was using is available.
If you want to try to shift which IRQ the onboard uses, you must free up the IRQ it was using, first, load Windows at least once, and have other IRQs available, then enable the USB in the bios again. I know from doing that I can get the onboard USB to use IRQ 12, which many cards can't use, other than some network cards. .
E.g. My 98SE computer was made in Aug 1999, has a 2000 bios update version, the Epox mboard has an Award bios.
Under PNP / PCI Configuration
Assign IRQ to USB - Enable / Disable - Disable that - that may be all it takes, but you may have to disable both settings.
Under Integrated Peripherals
Onchip USB - Enable / Disable - Disable it - if only that is disabled, the IRQ the USB is using will probably not be released for other uses.
Also under PNP / PCI Configuration
Assign IRQ to VGA - Enable / Disable - that does not need to be enabled unless you need video in a true Dos mode, but disabling it may make no difference in Windows regarding what IRQ the video uses.
PNP OS installed - Yes / No - you could try setting that opposite of what it was set to.
Resources controlled by - Auto / Manual
If you select Manual, you can assign any IRQ to Legacy or PNP.
E.g. assign IRQ 3, 4, and 12 to PNP use if they're set to Legacy by default.
Slot 1 - Auto, or specify an IRQ.
However, assigning an IRQ doesn't guarantee that the card in a slot can use that IRQ.
The ATX mboard has 7 card slots (8 in all) - 5 PCI, 2 ISA, one slot space is shared - for either an ISA or PCI card. One PCI slot (next to the AGP slot; no onboard video) shares it's IRQ with the video. One of the other slots uses the same IRQ as the video too.
I've never been able to use all the slots - not enough IRQs. Several identical USB cards might be able to use the same IRQ, other than that, it's impossible to use them all.
Chipset Features Setup
Video bios cachable - Enable / Disable - should always be enabled.
System bios cachable - Enable / Disable - should usually be enabled on an older mboard - the mboard will boot a bit faster, if nothing else.
"About the power supply...well there's a great possibility that it won't be a bolt on either. See the pic: ..."
Okay, so the case does not have the typical large hole, and the mounting is recessed a bit. Is the side of the PS facing those holes in the case a standard size ? Does the fan opening, and at least the top top holes for screws shown in your picture, line up with a regular PS ? If so, do you have or can you borrow a bimetal hole saw or two ?, to accomodate where the cord socket is on a regular PS ?
If the whole case is a standard size, you could transfer the board with it's components and wiring from the regular PS to the original case, the screw holes, fan, cord socket, and red 110/220 switch would of course line up. If the mounts for the board can be rigged so the board can be mounted, you would only need to unsolder / re-solder to the red 110/220 switch and the cord socket - the fan may have a connector on the end of it's cord in both cases - if not, remove the fan along with the board from the regular PS.
E.g. if the mounts in the orgininal case don't line up with the screw holes on the regular board, saw them off on the inside, or break them off using a vicegrip, places that have electronic parts often have hollow metal spacers, or use pieces of small diameter pipe, or drill out the orginal spacers, drill holes thru the case bottom where the mounts need to be, install machine screws long enough to pass through the case exterior thru the spacers to the board, install nuts, possibly washers, next to the board.
"Also I tried to find out if there is any way to overclock the processor ....."
Don't bother. Your greatest bottleneck is with the video, not the cpu.