|Yeah, if you did the format/s then the drive is empty except for the dos boot files and whatever files you added after the fact. |
If those files are the 98 setup files then you just need to type SETUP and enter in the directory the files are in. If you get some kind of memory error then you'll need to create a CONFIG.SYS file and have it load HIMEM.SYS. Then reboot and run SETUP again.
A lot of software is installed via a SETUP command. So even if there is a file named setup.exe it may be for something else and not a windows 98 file.
I'm not sure what you mean when you say the 'computer isn't recognizing any drives'. It must be booting up to a C:\> prompt so that drive is there and you say you copied some files from D: so that one is there. If you mean CD or DVD drives then yeah, you need to load a dos cdrom driver in CONFIG.SYS and MSCDEX in AUTOEXEC.BAT. After that dos should recognize them.
If you have a regular 98 installation cd it should be bootable and if your bios has the option to boot from cd then that would be the easiest way to do the installation.
If you can't boot from the cd then the next easiest way would be to use a 98 floppy bootdisk to start the installation. It will have cdrom drivers and you can start the install from cd once you boot from it.
But if you think you have all the files you can try the SETUP command I first mentioned and see what happens.