Well I recall trying to understand how this works previously, basically I think your answer is going to be USB.
whats your plan with using 3.5" disks? are you planning to use some sort of mac formatted, amiga formatted or PC?
Basiscally you can get a usb floppy drive for the PC so I would imagine theres a way to get that working (although I havent tried it myself yet and I have tons to learn about the pi yet), I dont know if CD drives work off the usb hub yet, (still learning) but basically I think if you plug in a powered usb hub inside your case you can add wifi/bluetooth/a hard drive/ other usb stuff.
As for the keyboard you can get a USB to ADB convertor, I have seen them online before as I think I was researching something to do with a connector on the back of an IMac monitor and you can get a usb to double ADB connector.
I just looked up an apple 3, man thats some old machine!
Sounds like your project is possible with a ton of usb convertors and stuff, good luck
