Bad idea to put the 4040 in, you will have to hack the tray by cutting good sized square that i would guess is about a 3x4 inch above the cpu slot and under the floppy. I imagine the floppy drive won't be able to be properly mounted.
3040's fit perfectly. They seem to be much rarer then the 4040, and harder to find But they are designed for the 3000D.
I have a WE 3040, and it is the best engineered accelerator for the 3000 I have come across. For anything other than heavy math, it was faster in day to day usage than my CS MK II 060@50. I bet you will pay close to a CS MKIII for a WE3040, but if you can find one I would buy it on the spot.
My advice look for a CS MK III or a WE 3040 for a 3000D. I did see a mercury board on Ebay awhile ago. That would be a good third or forth choice. It doesn't have Fast SCSI like the WE 3040 and CS MK III but, it fits without destroying the 3000D. The CS MK II, is ok also, you can't add the SCSI module, and really it isn't as nice as the others IMHO, but they seem to be more available.
For a few hundred more dollars, you buy something that is designed to fit and will not provide lots of grief and give a great experience in usage. If you have lots of spare time and are on a tight budget going with something else may work out for you, in the end it is always lots more work and headaches than anticipated, so in my old age I just count my pennies and buy the best option...
