Ugh...been building/repairing too many pc's lately...I assure you that I have linux (SuSE) on every intel box I own (though the one has windows as well for gaming...).
If it helps, I had to creatively alter my college computer desk to make room for my first amiga...it was too long for the hutch as it was an a1000, starboard II, and sidecar 1060 (with 10MB hard drive!). I actually had installed a csa accelerator in that box, but had to remove it because the 1060 was so timing dependent that the accelerator effectively killed it. My next amiga was an A500 with the Bodega Bay expansion chassis (again, too big for the desk!). Several 2000s followed...never had a 4000 though...and I kinda want an AmigaOne or Pegasos...but man are they pricey...
Regardless, I'll try a smaller drive (just picked one up off ebay) and see if that helps.
Dave