|Autoexec.bat and config.sys don't matter. The disk should boot without them as long as it has the correct mbr, the partition has the correct boot sector, and the necessary system files are there (and, I believe they have to be in the right place in MS-DOS 3.3). The most reliable way to do this is to format the partition then use the sys.com program to transfer the boot files from a floppy to the hard disk. After you have a bootable disk you can install the remainder of the files.|
If you can't boot after doing that then there is something wrong with your BIOS configuration.