Why are you trying to re-install Win98se, by deleting WIN.COM and doing the re-install from DOS mode? That's not exactly the best way to do an overtop re-install, generally-speaking. I would recommend booting off of a Win98se DOS-mode boot-floppy first (you DID make a "recovery disk"/"EBD" when prompted the first time that you installed Win98se, didn't you?), and running both SCANDISK /ALL and possibly doing a surface-scan, and assuming that all checks out OK, then also do a SCANREG /REPAIR, which will repair your system-registry if it has gotten corrupted.
At that point, hopefully you can boot Win98se, at least in Safe Mode, and then can run SFC.EXE (System File Checker), and perhaps that will find any corrupted system-file binaries. If you cannot boot, then tell us what the error message is.
The problem with doing an overtop re-install from DOS mode is, there is a backup of the very first system registry hive, called "SYSTEM.1ST", located in the root of C: (usually), with HSR attributes so it is also normally invisible. However, doing the overtop install, will then replace that original backup with, IIRC, a modified version that is a combination of your existing registry (including any potentially-problematic device-driver references), and the overtop re-install process (which resets default user/desktop settings, etc. and re-runs the hardware-detection phase).
So if you have some sort of system (SYSTEM.DAT) registry entry that references a device-driver during load that is problematic, a DOS-mode overtop re-install will likely NOT get rid of it. A better idea, is to go into the C:\WINDOWS\SYSTEM\IOSUBSYS and \VMM directories, and note any VXD files that have date/time stamps different from the release-date of the OS itself. (IOW, they are likely 3rd-party files.) If you, one-by-one, rename those to .VX~ or something like that, they will NOT load during bootup, although you may get an error (really a warning) mentioning that a device driver reference by the registry failed to load at boot. Hopefully, you can use that method to track down the problem, which is a pretty common one, of bad/conflicting VXDs during boot.
Good luck, report back if you can.