First off, The Amiga 4000 can not use Kickstarts 1.3 or 2.x, as someone suggested, Only 3.0/3.1 will work. No need to upgrade at this point, unless you want OS 3.9. But first things first...
Second, you will need to get a IDE Hard Drive. I would get a 20GB if you can but nothing larger. You will only be able to use up to 4GB for now, until you get up and running and then you can install patches, or the updated OS 3.9, to use the whole 20GB.
Thirdly, you will need a set of working AmigaDOS 3.0/3.1 install disks. And assuming your floppy drive works, you will be able to install the OS on the HD. If your floppy drive is TU (Tango Uniform, ie dead) you will need to get a replacement Amiga floppy drive! A PC one will not work without special mods. A replecement 4000 HD drive will cost you some cash! For some reason they are great investment items these days! lol If you can find a older Amiga 880k drive, that will do.
As far as the Cyberstorm MKII card, you will need to have a working setup then install the Phase 5 libs, then set the jumpers on the MB, (INT/EXT not sure which ones, try the opposite of what it's at now) then you can install the card. It sounds like you have a Rev D MB, as you have a built in CPU; a MC68030. (From your comments of 4000 working without CSMKII installed, and hand holding a disk)
Good luck,
