Large Hard Drive A4000D

[Oldsmobile_Mike]

As long as you're at BB2+ you should be fine working with partitions that large.  Better yet would be to reformat with PFS or SFS file system, but a proper install of 3.9 with the Boing Bags should be fine for working with partions of that size.

[Oldsmobile_Mike]

One big snag is that I don't have the original 3.9 CD for this installation.

Yeah, you'll need that.  The BB installers access files on the disk.  Fortunately you can still buy it new from many places:

http://www.vesalia.de/e_os39.htm

http://amigastore.eu/en/261-amiga-os-39.html

http://amiga.amedia-computer.com/index.php/catalogue/infos/1/4/ACF_AOS39

Also I recommend this, but your mileage may vary.  

[Oldsmobile_Mike]

(1) Sounds like it does, because it's working for you.  However there were a number of problems that were fixed by the Boing Bags.  Personally - if it were me - I wouldn't use the system without them.  It's the whole "just asking for trouble" thing.  Get the system running right, updated and stable, before using it for any critical work.  

(2) It validates against files on the disk.  Specifically some multimedia video files and a few others - a full list  was posted by someone else in another 3.9 thread a month or two ago.  The only difference might be if you have the pink ("Second Edition") or red pressing of the disk.

You should probably read this FAQ:  http://www.gregdonner.org/os39faq/os39faq.html