You have obviously managed to install your new hard drive (drive d: for example) as a slave to transfer files, so OK so far, but..
Start again. You need to make a Win98 floppy boot disk form your PC. Then install your new HDD as master, re-format using your floppy boot disk and then install windows 98.
When Windows is up and running, install your old HDD as a slave and transfer your files by dragging and dropping.
Post back if you have any problems.