I'm also switching to amiga so I might be able to help you here.
The Escom A1200s (the ones that you can get new) do have some motherboard fixes, but the disk drives aren't very good (i think they're pc ones), but it would be possible to get a proper amiga one from somewhere.
As you have a lot of money to spens, I suggest you get the Escom one, and a 68060 or a PPC, and put it in a tower. Most software was for the 68k so a '060 might be better, but a PPC will be the only option if you want to use OS4.
The '030 is also a nice processor. It runs cool enough to be usable in the desktop case (I think the '060 is cool enough as well), but the '040 (which isn't very compatible with most sofware) and the PPC will need a tower.
There is plenty of room for expansion in a desktop, viathe Expansion slot (underneath), clockport (inside), PCMCIA (on the side), IDE (inside). You can also add PCI cards using an adaptor if you have a tower.
As I have very little money to spens, I bought a used commodore A1200 and a Blizzard 1230 MKIV 50MHz with 128MB Fast RAM. It runs really nicely, even from floppy. I expect it will be nice with OS 3.9 and an HD.
Another advantage of the Esom ones is that you will have Kickstart 3.1. This means you won't have to upgrade the 3.0 roms in the commodore A1200.
I have used AmigaOS 3.9 in Amithlon and it is very nice, so you will have to get a copy. Luckely it is about £40 - a third of the cost of windows.
Hope that was useful.