There are some basic things in every CONFIG.SYS and AUTOEXEC.BAT and also some things that are unique to each installed program. Try to find and copy back the original installed DOS files before you put the Win 98 files on the disk and restore them. You can edit your AUTOEXEC.BAT and remove the @echo off command on the front and it will display each command as it is executed on your monitor. You can see which lines are getting errors and remove or correct them. Here are two typical files to look at.
AUTOEXEC>BAT
@ECHO OFF
PROMPT $p$g
PATH C:\DOS;C:\WINDOWS;C:\TOOLS
set sound= d:\sb
rem set sbmaster=4044-16656
C:\DOS\mode con: rate=30 delay=2
LH /L:0;1,45456 /S c:\dos\smartdrv 1024 256 /x
c:\tools\sa bold yellow on blue
c:\tools\numlkoff
LH /L:1,13984 C:\DOS\SHARE.EXE
CONFIG.SYS
DEVICE=C:\DOS\HIMEM.SYS
DEVICE=C:\DOS\EMM386.EXE NOEMS
BUFFERS=15,0
FILES=20
dos=UMB
LASTDRIVE=E
FCBS=16,8
dos = high
DEVICEHIGH /L:1,12048 =C:\DOS\SETVER.EXE
SHELL=C:\DOS\COMMAND.COM C:\DOS\ /p
DEVICEHIGH /L:1,19168 =C:\DOS\MSCMOUSE.SYS /2 /A9
STACKS=9,256
DEVICEHIGH /L:1,1824 =C:\DOS\TANSI.SYS
rem DEVICE=C:\WINDOWS\IFSHLP.SYS
If you edit the files to remove bad commands do not remove the lines. Instead, type rem on the front of the line and change them to remarks so you can restore them if need be.