patrik: Thanks for the input, I'll have to check out that link tomorrow. My setup is currently one internal HDD (original 100MB Quantum), an external Club Mac HDD (160 MB Quantum), and an external Micronet CD-ROM. The CD-ROM ID is set to 4, the Club Mac to 2, and the internal to 6. I looked at my motherboard and it looks un-terminated (missing resistor packs that are on the internal HDD). I had the Club Mac hooked up the 3000, and the CD-ROM hooked up to the Club Mac, with a terminator on the CD-ROM - so it sounds like what you described.
MrZammler: When you refer to using the correct jumper, do you mean the jumpers for setting the SCSI IDs?
motorollin: Thank you for the welcome, I'm glad to be here! I suspect a termination problem because of the chain of events that led me to my current situation. Notably, HDTools seeing my single internal HDD as 7 different drives. I'm far from a SCSI expert, so perhaps it's just wishful thinking.

I did disconnect all SCSI devices and I'm able to boot from a floppy. For further detail of where I'm at, see below.
Tahoe: On one hand it's nice to know that it's not just me having this problem, but on the other it's kind of depressing - it stings a bit to know that the 3.1 ROM upgrade I spent $180 (USD) on in 1999 is causing me problems.

I haven't tried softkicking anything besides 1.3 and 2.x, but I might give that a go if nothing else seems to work. You never know what'll help with this A3000 SCSI voodoo. hehe
Noster: I am using real 3.1 ROMs (Amiga Technologies GmbH), which is why I'm surprised by the troubles I'm facing. I've been suspecting that the SCSI driver in the 1.4 ROMs is different than the one in the 3.1 ROMs, but haven't read anything online to that effect. I have some extra cables to test out, so I'll give that a try as well. I would actually prefer to use the 3.1 ROMs vs. softkicking 2.x, if for no other reason than to gain 512 KB of fast RAM. I still don't have a passive terminator (should get one on Monday from a friend at work), but I did hook up a cable connected directly to the active terminator. Unfortunately my system still hung on boot.
I've been trying a lot of different things with my machine this afternoon and evening. To make a long story short: I disconnected my internal HDD and now I'm able to boot from a floppy. I hooked up my external HDD with a terminator, and I'm able to access it after booting WB from a floppy, and HDToolbox correctly reports only one SCSI device (ID 2). I was able to backup some of my more critical files to floppy, but I started getting a frozen system a few files in, so I'm still being cautious with that drive.
Does the 3000 write a SCSI device table to the HDD, or is that information stored in some kind of NVRAM, or is it generated on the fly at bootup? I was thinking that a corrupt SCSI table of sorts was written to my intenral HDD when I saved the six mystery drives in HDToolbox, and that's why my system is hanging...? If so, would putting that drive in the external enclosure allow me to boot from floppy and re-write the table? My A4000 motherboard is out for repairs right now, and I don't have a SCSI controller for it anyway. Perhaps I could peform a low-level format with x86 Linux, and then reinstall the drive on the Amiga to see if things are resolved...?
I'd like to say "THANK YOU!" to everyone here for taking the time to reply to my post. It's amazing and wonderful to get this kind of response for such an old system. I look forward to any replies, and I'll certainly keep you all updated on any progress I might make wtih the ol' miggy.