I'm gradually working on a similar tower build. I don't think I took any good "before" pictures of the tower case, which I regret now, but might be able to fake something useful together for that state of things.
The easiest way would be to buy a tower from Elbox, I think they sold one intended for this particular purpose. They did for a couple models of Amigas anyway, but I'm not entirely sure about an A3000d tower from them.
But for building your own, it's a lot easier to get things lined up right if you have the Mediator from the start, so you can fiddle around with it plugged into the motherboard to see how things will be happiest.
The tower I have had the rear expansion slots on a slide-out panel that the PC motherboard attached to, so you could remove your motherboard with PCI cards still in place. A convenience that doesn't apply to most towers. I seperated this bracket panel from the PC motherboard panel so I can fiddle with the two seperately, but both pices will be used in the end.
The rear expansion slots piece is being merged with the original A3000d frame. I'm going to leave the motherboard in the original frame (no pretty lid though, that's gone), and I've dremelled the A3000 frame quite a bit to allow access to the tower's rear brackets panel which I attached to the old frame with a couple screws. I plugged in the Mediator 3000 and some junk PCI cards to learn where the tower expansion brackets needed to go exactly. I'm going to need to dremel this but of the tower as well as the tower frame some to get things to fit back together there well again, and will need to fill some seams with epoxy putty.
To do that much I cut off the front side of the A3000d frame so it's no taller than where the A3000 motherboard there is, and I cut off the back of the A3000d frame above the serial/parallel/SCSI/etc. holes. This gets that metal out of the way for PCI cards to reach the tower rear brackets panel. Also, the A3000d bracket which holds the pwoer supply and hard and floppy drives is gone.
The old tower PC motherboard panel needs some new mounting brackets added to the tower frame so it will be held sturdy, and the remaining A3000d frame will be screwed to this tower panel. I'll add some other screws or something in the rear expaneion brackets area someplace to help make that stuff sturdy as well, but I haven't yet figured that part out.
I've removed all drive cage stuff from teh tower frame, as well as the cross bar from front to back of the frame as all that was in the way of the A3000d. I'll put these back in when the motherboard area is more complete so I know how many drive bays will fit back in. I'll ahve to cut off the bottom couple bays from the drive cage pieces for everything to fit.
I haven't yet figured out what to do about the power supply either. I've towered an A500 and an A2000 before, but don't yet know if I can do the same things there or not. Those used an AT power supply which I'm not sure where to get now, it's all ATX today. There may be something on aminet about this, and someone on one of these Amiga sites had a fwe months ago asked abotu interest for power supply adaptors, but I haven't heard since if he ever made any. (I'd buy a couple!)
I haven't done anything with this project for a couple months now, other things have taken priority. I'd like to finish it up so I can clean up the parts all over my living room for it, and my A3000d is currently quite an ugly mess piled up the way it is on my computer desk and I'm afraid to use it since the power supply, floppy drive and hard drive are all kindof balancing in a pile.
When I get back to it someday I'll snap some pictures and make up a hack doc to put on aminet. I've got an A2000T.lha file there already which might give some ideas as well, but that put the A2000 motherboard directly to the tower's PC motherboard plate with some newly made screwholes, and the tower's expansion brackets pretty much lined up already, I just had to put the new mounting screws in just the right places and have the right amount of height above the tower's PC motherboard panel. That might be possible with A3000d if you leave out the original A3000 frame, but for some reason I decided to do it different this time around, mostly to keep the A3000 frame's rear connector holes and labels.
Yes, fitting an Amiga into a standard PC tower is a good bit of work!
P.S. This may give some ideas, but the details are highly specific to the tower case in question, so you might find you are better off with a somewhat different approach to the problem.
