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I'm going to guess that's Kickstart 2.1? (1.2 would have been the original kickstart, if you bought the machine in 1987/88, or so.)
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It's Kickstart 2.1 yes, and it has a software load of Kickstart 3.1. Can you still get the 3.1 roms? Ebay right? =)
Ebay, umm... Software Hut might have them as well. Make sure that they are ROMs for an A2000 (and A500 I think).
It is also possible to softkick the rom into RAM. Umm, however, that means you need to get the ROM file (legally you can get them from Cloanto as part of their Amiga Forever package along with the OS I think) but that involves you mucking about with your start up script, additional reboots, and its generally not all that pleasant.

Along those lines, I see you need a CD ROM for 3.9, I have a SCSI burner lying around doing nothing will this work?
It should work, but ironically, you'll need to have access to a CD Filesystem. (There is one included with OS3.9 AFAIK). You can use this:
AmiCDFS on aminet to get you started.
The annoying part is how do you transfer it to your amiga.

There is a program called CrossDOS (included in 3.1) that would allow you to read DOS formatted 720k floppies. If you have a terminal program on your amiga and a null-modem cable, you can at least do some of the work that way. You might also be able to use
fat95 from AmiNet to read PC formatted floppies (but you still have to install it on your amiga.

)
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Ouch! You definitly need RAM. A cheap thing to pick up on eBay might be a processor upgrade with local FastRAM. A card with a 68030 @ 25mhz with 4 or 8MB FastRAM on it should only go for about $50, and give you a HUGE performance and function boost.
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I'll look for one. Are there better ones? Is there a place I can get a rundown of what is available and what they do?
There are 040 and 060 cards out there but they'll be a tad expensive. I beleive the card in question is the
A2630, it's an official Commodore-made expansion. I've used it in the past and it's pretty good.

Here's some
eBay search results.I have a HD in it currently, so I'm guessin it has a SCSI controller. If I need an additional one, I have a bunch of ISA SCSI controllers lying around collecting dust. Can I install one of these?
Most controllers that came with the A2000 are SCSI controllers. You won't be able to use the ISA controllers right away as you'd need a bridgeboard or something like the GoldenGate2 or CrossLink. Here's a
list of cards that might be able to allow you to use ISA.SCSI cards should be able to handle 7 devices (provided that the chain is properly terminated and you don't use a overly large cable.)
Good luck!