Not sure what you intend to do with your A3000 but I can certainly throw in my two cents regarding recommendations. I run this machine myself.
1) fill up to 16mb ram on motherboard if possible.
2) additional ram available via some fast slot based accelerators or the new Zoram product. It is all a question of money.
3) Good deal on you already having the 3.1 kickstarts.
4) Modem? not sure. recommend standard ethernet upgrade. X-surf is a zorro based ethernet card and also includes 2 clockports (a nifty side feature)
5) I see former post about Deneb USB. This is the best Zorro based USB solution hands down. You will really like having USB ability on an Amiga. I run a clockport based Subway USB setup. Not as slick as Deneb but it does work just fine.
6) As far as hard drive, you can probably find plenty of larger SCSI drives out there for little to no $. There are modern possibilities as well. One such possibility is mentioned above (ACard adapter). I believe they have SCSI to either ATA or SATA conversion models. Now you can buy a brand new drive. There is also an Elbox Fast ATA Zorro card. I have an older model. It works fine...just takes Amiga a little longer to boot up the first time (loading drivers, starting the CDFS, etc...) After that it is great. I see they have a new version of this card that has multiple drive capability; ATA, SATA, Compact Flash). Wish I had that one.
7) I elected to go with an RTG video card. It is a GVP Spectrum 24/28. While not the best card there is, it works great. Indivision ECS is another possibility if you want to stay in ECS based video.

Accelerators are harder and more expensive to come by. I use a A3640 v3.1 which is a fairly generic 68040-25mhz and has FPU. It was cheap and does run faster than the original 68030 did.
Enjoy that A3000. Not many people have these machines or even like them because they are not AGA based. AGA does not matter to me, the A3000 is a very expandable big box Amiga and a real decent machine overall. Have fun with it.