Of course I'm in the middle of a big deadline, so this is how I'm spending my time. Oy. I'll never learn.
Regardless...
Yeah. You're right. The unpopulated sockets are probably a red herring I shouldn't even consider...
More clues:
Clue 1:

Bootup sequence colors. Regular colors not happening. I get black screen with stripes before I get the enter disk screen (or WB screen if booting from floppy.) According to Castellen's page that points to a ROM/CIA issue. How to go forward with this? Order new ROMs? Call the CIA? The FBI? Oy bad joke.
Clue 2:

Battery: Reading up on this, the battery, if not working, could be a source of SCSI woes. I attempted the setclock command, which, when used without arguments gave me no error, which I think would seem to say the battery is ok. For a second opinion, I ran the time prefs program off the 3.1 extras disk. The time was set to sometime in 1994. I changed the date and saved. I powered down the computer, and unplugged the power from the PSU. I rebooted. It seemed to remember the new date. Does that prove the battery is operational? I may consider putting a new one in regardless. Maybe even the same kind since it looks like a solderless solution, and he's had put some slick velcro holding it in place.
Anyway... I hope I'm not babbling too much here and being a nuisance.. You don't hear from me for years, then I come on and bug the living daylights out of you.
edit:
if it is holding time, batt should be ok, just measure the voltage on it.
should of read closer before replying.. looks like you have it booting.. pull any all expansion cards out that are not needed. this will narrow things down.
seems you managed to boot a disk, do have you tried hdtoolbox?
you can swap the cia's with one another and see if symptoms change.
double check the part numbers on the roms, someone may have swapped in incorrect roms, its doubtful but it might happen. i had this problem on a a4000 someone put 1200 roms in, it booted but would never see fast ram
i have been an amigan since 87 and owned tons of 3000's and repaired many in the past, not saying i am some kind of expert but..... dont worry about the internal termination sockets for resistor packs, its better they are gone, just make sure you run a terminator on the last internal drive and a external terminator on the db25.
the battery does keep scsi prefs,mostly if its set to async or synchronous etc. It will default back to async when the battery was removed. it will run fine without the battery in almost every case. You can use setbatt.lha off aminet to set these prefs,of course if you can't boot the machine you cant set this.
Check the western digital scsi chip, the latest has a -08 in the part number at the end, or it can be a amd 33c93a.. proto does not matter as long as its either of the ones i mentioned. the 04 and earlier ones have problems with more than 1 hd sometimes but should work with 1 drive . check for term power,you are looking for close to +5v- on the external scsi connector its pin 25,internal 50 pin connector i *think* its pin 26(please verify this first!).. BE CAREFUL! any shorts could kill it and ruin your day. without term power terminators do not work. if no power, check diode d800 i think it is,some are shorted,some open,some installed backward on some boards.
you need to get a working floppy on it, then boot with a install disk and run hd tools to look at the hard drive partitions and or partition/format the drive. if the current HD isnt set to bootable or the filesystem is messed up,it wont do much.
Good luck and keep us posted!
Mech