Well, sorry for not getting back sooner with my results but real life gets in the way sometimes.

Anyways, I have spent numerous hours on this and still haven't made any progress. I am not sure if it is a sporadic hardware issue or what but I just can't get OS3.9 installed. I am literally ready to pitch my Amiga gear onto the trash-heap of time.
I set up 3.9 in WinUAE and it works flawlessly on a CF card. I move it to the real amiga and it won't boot up. It just loads up to a black screen and sits there.
So, I figured that I would follow Cammy's advise and do a .lha archive on WinUAE and then transfer the good OS3.9 install to my A3000 that way. I create the .lha archive fine on uae with no problem. I then transfer the CF card to my A3000 and everytime I try to unarchive the backup.lha it fails with a 'Failed CRC Check' at a different spot everytime.
So.... Back to installing OS3.0 of off the CDROM the old way.
* I install 3.1 onto the boot drive of the A3000...... no problem.
* Move CD0: to Devs, double-click it and my CDROM shows up fine.
* Reboot, CD0: causes a suspend message and locks up workbench.
* Reboot with bootdisk, move CD0: out of Devs, reboot 3.1 install fine.
* manual mount CD0: again, to access OS3.9 CD, fine.
* Proceed to make Emergency-Disk, install fails with c/installer crash.
* Reboot, CDROM drive not recognized.
* Reboot, CDROM shows up, try to make Emergency-Disk again, installer abruptly quits back to workbench about half-way thru making e-disk.
*Boot E-disk, flashes something about iprefs:bad loadfile hunk but gets to workbench
*WB3.1 install on internal SCSI HD now showing checksum errors.
*Start OS3.9 installer from CDROM, Installer crashes with c/installer program failed.
* Reboot E-disk, now it crashes with a datatypes error.
etc.
Memories come flooding back why I dumped the Amiga for PC back in 1992!

Ready to give up.......