First of all, you might have a copy of system.ini in some other form still on your drive. If you ever used "sysedit" to edit the system.ini file, you'll automatically have a copy of system.ini named "system.syd". You can rename system.ini and then rename system.syd to system.ini.
Look in your c:\windows folder for any file that starts with "system."
The initial copy of your registry is named system.1st That's certainly not a system.ini backup. Look for something less than 20KB as a file size, generally speaking. Then look at it with Notepad, and see if it's a backup of system.ini.
In the meantime, if no such file exists, my newly installed version of Windows98SE on a clean hard drive has left me with a generic version, more or less, of system.ini. It has basic entries in one particular section that lists device drivers that's causing you problems. So, just look at my list, then look at your list in the same section in your system.ini, and put a semi-colon in front of any line that doesn't appear in mine and DOES appear in yours:
The section is "[386Enh]" (no quotes):
[386Enh]
ebios=*ebios
woafont=dosapp.fon
device=*dynapage
device=*vcd
device=*vpd
device=*int13
device=*enable
keyboard=*vkd
display=*vdd,*vflatd
mouse=*vmouse,msmouse.vxd
If your [386Enh] section has additional lines, put a ";' in front of the "device=" line so it reads ";device=" (no quotes)
If you still get errors, make a note of what they are and what section of System.ini they appear in and list them here.